From promos at global-submit.com  Fri Sep 24 06:33:27 2004
From: promos at global-submit.com (promos at global-submit.com)
Date: Fri, 24 Sep 2004 06:33:27 -0400
Subject: [EMBOSS] Special Ends Soon...
Message-ID: <200409241033.GAA10971@sg8.global-submit.com>

You are receiving this e-mail because you were added to
http://www.global-submit.com in the past. Here is the URL
that was submitted to our search engine database.
http://bioinfo.pbi.nrc.ca:8090/EMBOSS/index.html

Start your Christmas advertising now. Get
your banner viewed accross our network
of over 80,000 different web pages.
During the Early Bird Special when you 
order 1 million exposure, we will double
your account at no extra charge. This
special applies to accounts activated 
before October 31st.

For more information, please visit our web
site at http://www.bannerscape.com or
gove me a call at 1 819 571 4943, 24
hours a day 7 days a week,  for more 
information

Thank you and have a nice day,

William Hanks
http://william.global-submit.com
william at global-submit.com
Call 1 819 571 4943 at any time.





RMV MESSAGE ID : T837098R53791

If would like to be taken out of our database then please visit this web site.
http://www.global-submit.com/cgi-bin/clipout.cgi?T837098R53791



From kellert at ohsu.edu  Thu Sep  2 22:52:55 2004
From: kellert at ohsu.edu (Thomas J Keller)
Date: Thu, 2 Sep 2004 19:52:55 -0700
Subject: [EMBOSS] backtranseq with ambiguities
Message-ID: <5B16DE52-FD54-11D8-A523-0003930405E2@ohsu.edu>

Greetings,
Is there a way to back translate a protein sequence and get a family of 
DNA sequences representing the possible gene sequences?

Thanks,
Tom K.

Tom Keller, Ph.D.
http://www.ohsu.edu/research/core
kellert at ohsu.edu
503-494-2442
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From kellert at ohsu.edu  Fri Sep  3 17:30:56 2004
From: kellert at ohsu.edu (Thomas J Keller)
Date: Fri, 3 Sep 2004 14:30:56 -0700
Subject: [EMBOSS] withrefm and proto for rebaseextract
Message-ID: <8A920A60-FDF0-11D8-8B08-0003930405E2@ohsu.edu>

Greetings,
The files available at http://rebase.neb.com/rebase/rebase.f37.html 
which offers the EMBOSS format rebase files, don't look like the input 
files (withrefm and proto) shown in the documentation. Which is which?

Thanks,
Tom K.

Tom Keller, Ph.D.
http://www.ohsu.edu/research/core
kellert at ohsu.edu
503-494-2442
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From David.Bauer at SCHERING.DE  Mon Sep  6 01:29:06 2004
From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE)
Date: Mon, 6 Sep 2004 07:29:06 +0200
Subject: Antwort: [EMBOSS] withrefm and proto for rebaseextract
Message-ID: <OFE94D0453.C22C2DE8-ONC1256F07.001DA1F6-C1256F07.001E228D@schering.de>


Hi Tom,

you can find the withrefm and proto files on the ftp server:
ftp://ftp.neb.com/pub/rebase/
The program rebaseextract creates from the 2 input files the emboss format
files embossre.enz, .ref and .sup and places them in .../data/REBASE.
The 3 files in format 37 are already reformated, so you don't need to run
rebaseextract but just rename them and copy in the emboss data directory.

David.



                                                                                                                           
                      "Thomas J                                                                                            
                      Keller"                                                                                              
                      <kellert at ohsu.ed         An:      emboss at hgmp.mrc.ac.uk                                              
                      u>                       Kopie:                                                                      
                      Gesendet von:            Thema:   [EMBOSS] withrefm and proto for rebaseextract                      
                      owner-emboss at hgm                                                                                     
                      p.mrc.ac.uk                                                                                          
                                                                                                                           
                                                                                                                           
                      03.09.2004 23:30                                                                                     
                                                                                                                           
                                                                                                                           




Greetings,
The files available at http://rebase.neb.com/rebase/rebase.f37.html
which offers the EMBOSS format rebase files, don't look like the input
files (withrefm and proto) shown in the documentation. Which is which?

Thanks,
Tom K.

Tom Keller, Ph.D.
http://www.ohsu.edu/research/core
kellert at ohsu.edu
503-494-2442






From mad at biol.unlp.edu.ar  Wed Sep  8 09:57:45 2004
From: mad at biol.unlp.edu.ar (Martin Sarachu)
Date: Wed,  8 Sep 2004 10:57:45 -0300
Subject: [EMBOSS] wEMBOSS-1.2
Message-ID: <1094651865.413f0fd9bb538@nahuel.biol.unlp.edu.ar>

This is to announce the release of wEMBOSS version 1.2

Some of the improvements are:
- Upgraded for EMBOSS-2.9.0
- Improved handling of project results for better performance

wEMBOSS is available for downloading on the wEMBOSS Portal
http://www.wemboss.org or download it using this link
http://www.wemboss.org/Folder.2003-09-11.4050/Folder.2003-09-11.4318C/wEMBOSS-1.2.tar.gz
Please post all your comments, suggestions and problems on the wEMBOSS forums
available on the Portal.

Enjoy wEMBOSS! 

-- 
Mart?n Sarachu
msarachu at biol.unlp.edu.ar
EMBnet Argentina
http://www.ar.embnet.org


From bioinfovijayaraj at yahoo.com  Fri Sep 10 03:52:14 2004
From: bioinfovijayaraj at yahoo.com (vijayaraj nagarajan)
Date: Fri, 10 Sep 2004 00:52:14 -0700 (PDT)
Subject: [EMBOSS] user-profile-regarding
Message-ID: <20040910075214.68385.qmail@web53606.mail.yahoo.com>

hi friends

i created a user with default BASH shel.
i created another user with default CSH shel.
i have set the path of the PLPLOT_LIB in the
/etc/profile


now..the problem is ...i could execute the text based
emboss programs in both the user prompts.

But, when i try to save the output in PS or in PNG
format...(X based...), then i could do this only in
the user who has BASH by default. 
i get the error (set path error), when i run the same
program with the other user, whose default shel is
csh.

we have gcg wisconsin also running in the same server
and the user need csh . so, if i change the shell from
default to bash, after logging in...even then i
couldnt run the x based outputs.....

pls help me to solve this problem.
i need to run both gcg and emboss from the same user.

i couldnt also set the environment after logging in to
the users...as i get the command not found error..in
the users...but not with the root.

pls help.
thanks in advance.
regards
vijay


	
		
__________________________________
Do you Yahoo!?
New and Improved Yahoo! Mail - 100MB free storage!
http://promotions.yahoo.com/new_mail 


From smarkel at scitegic.com  Fri Sep 10 13:23:24 2004
From: smarkel at scitegic.com (Scott Markel)
Date: Fri, 10 Sep 2004 10:23:24 -0700
Subject: [EMBOSS] difficulty using databases and "water"
Message-ID: <4141E30C.7000207@scitegic.com>

I'm using 2.9.0, built in cygwin, running in Windows XP.
I'm having problems creating databases for use with "water".

I created a USA database using dbifasta.

133 > dbifasta -idformat idacc -directory /C/SandBox/EMBOSS -filenames NRDB_protein_10.* -dbname NRDB_protein_10 -release 1.0 -date "10/09/04" -fields acnum -fields des -fields seqvn
Index a fasta database

I edited ~/.embossrc to include the new database.

134 > cat ~/.embossrc
DB NRDB_protein_10 [
    type: P
    format: fasta
    method: emblcd
    fields: "id acc sv des"
    directory: /C/SandBox/EMBOSS
    indexdirectory: /C/SandBox/EMBOSS
    file: NRDB_protein_10.fa
]

showdb does the right thing.

135 > showdb
Displays information on the currently available databases
# Name        Type ID  Qry All Comment
# ====        ==== ==  === === =======
NRDB_protein_10 P    OK  OK  OK  -

seqret can access all of the database.

136 > seqret NRDB_protein_10:\* stdout
Reads and writes (returns) sequences
 >XP_357594.1 XP_357594.1 similar to KIAA0960 protein [Mus musculus]
MCFPGEEVDRQLCRDAIFPIPVACDAPCPKDCVLSAWSSWSSCSHTCSGKTTEGKQTRAR
<shows all 10 sequences just fine>

I can't seem to access an individual sequence.

137 > seqret NRDB_protein_10:XP_357594
Reads and writes (returns) sequences
Error: Unable to read sequence 'NRDB_protein_10:XP_357594'
Died: seqret terminated: Bad value for '-sequence' and no prompt

What I'm really trying to do is run "water", but I expect
my database problems are impacting that.

161 > water -asequence query.fa -bsequence NRDB_protein_10:\*
Smith-Waterman local alignment.

    EMBOSS An error in ajarr.c at line 1805:
Token missing

Any pointers to documentation or examples would be greatly
appreciated.

Scott

-- 
Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at scitegic.com
SciTegic Inc.                       mobile: +1 858 205 3653
9665 Chesapeake Drive, Suite 401    voice:  +1 858 279 8800, ext. 253
San Diego, CA 92123                 fax:    +1 858 279 8804
USA                                 web:    http://www.scitegic.com




From d.m.a.martin at dundee.ac.uk  Mon Sep 13 12:36:08 2004
From: d.m.a.martin at dundee.ac.uk (David Martin)
Date: Mon, 13 Sep 2004 17:36:08 +0100
Subject: [EMBOSS] Sorting errors with DBIFLAT
Message-ID: <s145da9c.080@IA-GEN-A2.dundee.ac.uk>

I have been trying to index swissprot with DBIFLAT. For most sequences
it seems to work just fine, but for my pet sequence it fails, being
unable to find the sequence.

The reason is that it is sorting the list of IDs incorrectly before
writing them to entrynam.idx.

I wrote a short script to asciiify the entrynam.idx file and found the
appropriate entries.

Here is the excerpt:

ENTRY 1775562 :TFH3_HUMAN:475273634:0:1
ENTRY 1775563 :TFH3_MOUSE:475279037:0:1
ENTRY 1775564 :TFH4_HUMAN:475283197:0:1
ENTRY 1775565 :TFH4_MOUSE:475288725:0:1
ENTRY 1775566 :TFH4_PANTR:475293031:0:1
ENTRY 1775567 :TF_HUMAN:475515366:0:1
ENTRY 1775568 :TFL1_ARATH:475296099:0:1
ENTRY 1775569 :TF_MOUSE:475525712:0:1
ENTRY 1775570 :TFOX_HAEIN:475300602:0:1
ENTRY 1775571 :TFP2_HUMAN:475304815:0:1
ENTRY 1775572 :TFP2_MOUSE:475312007:0:1

This is most definitely not alphabetical order.

Any ideas on why/wherefor and fixes?

..d


From ableasby at hgmp.mrc.ac.uk  Mon Sep 13 14:05:27 2004
From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby)
Date: Mon, 13 Sep 2004 19:05:27 +0100 (BST)
Subject: [EMBOSS] Sorting errors with DBIFLAT
Message-ID: <200409131805.i8DI5RgU021092@bromine.hgmp.mrc.ac.uk>

This has just come up on emboss-bug and is a locale
feature (usually with GNU 'sort'). The solution
is to:
     setenv LC_ALL C

It has been known about for years. I expect we ought to put
it in the FAQ but it will become redundant when the new
indexing system is finished.

Alan


From Paul.Baumgartner at unibas.ch  Tue Sep 14 09:04:10 2004
From: Paul.Baumgartner at unibas.ch (Paul Baumgartner)
Date: Tue, 14 Sep 2004 15:04:10 +0200
Subject: [EMBOSS] primer3_core
Message-ID: <91E400FC-064E-11D9-8561-003065B9531E@unibas.ch>

Dear all

to generate primer3_core from primer3_1.0.0.tar archive the compiler 
generates the following Error:

  gcc -g -o primer3_core primer3_main.o oligotm.o dpal_primer.o 
format_output.o boulder_input.o '-static' -lm
ld: can't locate file for: -lcrt0.o
make: *** [primer3_core] Error 1

what could be wrong ?

( Mac OS 10.3.5 gcc 3.3)

thanks   Paul

Biozentrum
Paul Baumgartner
Zellbiologie
Klingelbergstrasse 70
CH-4056 Basel



From augereau at u540.montp.inserm.fr  Tue Sep 14 10:45:00 2004
From: augereau at u540.montp.inserm.fr (Patrick Augereau)
Date: Tue, 14 Sep 2004 16:45:00 +0200
Subject: [EMBOSS] building Emboss under cygwin
Message-ID: <414703EC.4030109@u540.montp.inserm.fr>

Hello,
I tried to build Emboss package in a cygwin environment, but after a
while, I got the following messages:

Creating library file: .libs/libajax.dll.a
.libs/ajgraph.o(.text+0x16):ajgraph.c: undefined reference to `_c_plschr'
.libs/ajgraph.o(.text+0x20d):ajgraph.c: undefined reference to `_c_plinit'
.libs/ajgraph.o(.text+0x278):ajgraph.c: undefined reference to `_c_plssub'
.libs/ajgraph.o(.text+0x3ce):ajgraph.c: undefined reference to `_c_plvpor'
.libs/ajgraph.o(.text+0x41b):ajgraph.c: undefined reference to `_c_plvsta'
.libs/ajgraph.o(.text+0x60b):ajgraph.c: undefined reference to `_c_pljoin'
.libs/ajgraph.o(.text+0x6d4):ajgraph.c: undefined reference to `_c_pljoin'
.libs/ajgraph.o(.text+0x963):ajgraph.c: undefined reference to `_c_plend'
.libs/ajgraph.o(.text+0xa99):ajgraph.c: undefined reference to `_c_plschr'
.libs/ajgraph.o(.text+0xaf4):ajgraph.c: undefined reference to `_c_plmtex'
.libs/ajgraph.o(.text+0xb25):ajgraph.c: undefined reference to `_c_plmtex'
.libs/ajgraph.o(.text+0xb56):ajgraph.c: undefined reference to `_c_plmtex'
.libs/ajgraph.o(.text+0xbb0):ajgraph.c: undefined reference to `_c_plmtex'
.libs/ajgraph.o(.text+0xf5e):ajgraph.c: undefined reference to `_c_plmtex'
.libs/ajgraph.o(.text+0x1fb6):ajgraph.c: undefined reference to `_c_plgpage'
.libs/ajgraph.o(.text+0x21a0):ajgraph.c: undefined reference to `_c_plbox'
.libs/ajgraph.o(.text+0x5bd1):ajgraph.c: undefined reference to `_c_plxswin'
.libs/ajgraph.o(.text+0x5c37):ajgraph.c: undefined reference to `_c_plxswin'
.libs/ajgraph.o(.text+0x6aee):ajgraph.c: undefined reference to
`_c_plfileinfo'
.libs/ajgraph.o(.text+0x3d):ajgraph.c: undefined reference to `_c_plstrlW'
.libs/ajgraph.o(.text+0x72):ajgraph.c: undefined reference to `_c_plgchrW'
.libs/ajgraph.o(.text+0xec):ajgraph.c: undefined reference to `_c_plsdev'
.libs/ajgraph.o(.text+0x1bc):ajgraph.c: undefined reference to `_c_plxsfnam'
.libs/ajgraph.o(.text+0x246):ajgraph.c: undefined reference to `_c_pladv'
.libs/ajgraph.o(.text+0x2ef):ajgraph.c: undefined reference to `_c_plwind'
.libs/ajgraph.o(.text+0x4f9):ajgraph.c: undefined reference to `_c_plline'
.libs/ajgraph.o(.text+0x75e):ajgraph.c: undefined reference to `_c_plfill'
.libs/ajgraph.o(.text+0x7d6):ajgraph.c: undefined reference to `_c_plscol0'
.libs/ajgraph.o(.text+0x84a):ajgraph.c: undefined reference to `_c_plpoin'
.libs/ajgraph.o(.text+0x9ff):ajgraph.c: undefined reference to `_c_plptex'
.libs/ajgraph.o(.text+0xa36):ajgraph.c: undefined reference to `_c_pllsty'
.libs/ajgraph.o(.text+0xa66):ajgraph.c: undefined reference to `_c_plpsty'
.libs/ajgraph.o(.text+0xbf6):ajgraph.c: undefined reference to `_c_plcol0'
.libs/ajgraph.o(.text+0xc3b):ajgraph.c: undefined reference to `_c_plwid'
.libs/ajgraph.o(.text+0x123b):ajgraph.c: undefined reference to
`_c_plxtrace'
.libs/ajgraph.o(.text+0x1f20):ajgraph.c: undefined reference to `_c_plgchr'
.libs/ajgraph.o(.text+0x2026):ajgraph.c: undefined reference to `_c_plsori'
.libs/ajgraph.o(.text+0x266e):ajgraph.c: undefined reference to `_c_pljoin'
.libs/ajgraph.o(.text+0x2ad4):ajgraph.c: undefined reference to `_c_plerry'
.libs/ajgraph.o(.text+0x2b64):ajgraph.c: undefined reference to `_c_plerrx'
collect2: ld returned 1 exit status
make[1]: *** [libajax.la] Error 1
make: *** [all-recursive] Error 1

What is missing in my cygwin install ? I tried to build under linux, and
all went fine, but with cygwin I always failed, whatever package I had
to the environment.
Thanks in advance for any help.

-- 
Patrick Augereau
Inserm U540
tel: 33 (0)4 67 04 37 13
fax: 33 (0)4 67 54 05 98


From ableasby at hgmp.mrc.ac.uk  Tue Sep 14 11:25:59 2004
From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby)
Date: Tue, 14 Sep 2004 16:25:59 +0100 (BST)
Subject: [EMBOSS] building Emboss under cygwin
Message-ID: <200409141525.i8EFPx3f029112@bromine.hgmp.mrc.ac.uk>

Others may be able to give more specific help regarding
individual packages that may need updating. If you
completely delete cygwin and reinstall the latest version
then it will work. The errors refer to changes made to
both cygwin and EMBOSS to enable production of shared
libraries on that system. If you want to experiment I'd
look in the gcc/ld(bintools)/make area.

HTH

Alan Bleasby


From Paul.Baumgartner at unibas.ch  Tue Sep 14 12:30:08 2004
From: Paul.Baumgartner at unibas.ch (Paul Baumgartner)
Date: Tue, 14 Sep 2004 18:30:08 +0200
Subject: [EMBOSS] primer3_core
In-Reply-To: <812BE26A-0661-11D9-B741-000393C44276@cgt.mc.duke.edu>
References: <91E400FC-064E-11D9-8561-003065B9531E@unibas.ch> <812BE26A-0661-11D9-B741-000393C44276@cgt.mc.duke.edu>
Message-ID: <575D1B6C-066B-11D9-8561-003065B9531E@unibas.ch>

I removed (#LIBOPTS ='-static') from the Makefile and the compiler 
generated primer3_core, cp to /sw/bin and run eprimer3 :
works for stdout
but outputfiles :
Output file [hsfau.eprimer3]:
Error: Unable to open file 'hsfau.eprimer3' for output
Output file [hsfau.eprimer3]: prim.txt
Error: Unable to open file 'prim.txt' for output
Died: eprimer3 terminated: Bad value for '-outfile' and no more retries

what commands are used for fink (the archive primer3_1.0.0.tar I have 
here)?

I installed emboss 2.8.0 by fink commander, but it seems that the 
component primer3_core is missing

thanks



On 14.09.2004, at 17:19, Jason Stajich wrote:

> Try removing the the '-static' from the makefile.
>
> This is final stmt to build primer3_core that works for me on OSX.
>
> gcc  -o primer3_core primer3_main.o oligotm.o dpal_primer.o 
> format_output.o boulder_input.o  -lm
>
> fink can build primer3 just fine so you may try that. There is also a 
> fink emboss pkg too.
> -jason
>
> On Sep 14, 2004, at 9:04 AM, Paul Baumgartner wrote:
>
>> locate file for: -lcrt0.o
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>
>
Biozentrum
Paul Baumgartner
Zellbiologie
Klingelbergstrasse 70
CH-4056 Basel



From kvddrift at earthlink.net  Tue Sep 14 18:39:46 2004
From: kvddrift at earthlink.net (Koen van der Drift)
Date: Tue, 14 Sep 2004 18:39:46 -0400
Subject: [EMBOSS] primer3_core
In-Reply-To: <575D1B6C-066B-11D9-8561-003065B9531E@unibas.ch>
References: <91E400FC-064E-11D9-8561-003065B9531E@unibas.ch> <812BE26A-0661-11D9-B741-000393C44276@cgt.mc.duke.edu> <575D1B6C-066B-11D9-8561-003065B9531E@unibas.ch>
Message-ID: <FA714CB8-069E-11D9-A857-003065A5FDCC@earthlink.net>


On Sep 14, 2004, at 12:30 PM, Paul Baumgartner wrote:

> I removed (#LIBOPTS ='-static') from the Makefile and the compiler 
> generated primer3_core, cp to /sw/bin and run eprimer3 :
> works for stdout
> but outputfiles :
> Output file [hsfau.eprimer3]:
> Error: Unable to open file 'hsfau.eprimer3' for output
> Output file [hsfau.eprimer3]: prim.txt
> Error: Unable to open file 'prim.txt' for output
> Died: eprimer3 terminated: Bad value for '-outfile' and no more retries
>
> what commands are used for fink (the archive primer3_1.0.0.tar I have 
> here)?
>
> I installed emboss 2.8.0 by fink commander, but it seems that the 
> component primer3_core is missing

Paul,

Primer3 is not present in fink right now. And as you can read in the 
eprimer3 docs it needs to be installed separately, so it not missing 
from the emboss package.

The above errors indicate a privileges problem, I suspect because you 
copied primer_core into /sw/lib. Remove it from /sw/bin and put it in 
/usr/local/bin, and try again. I am not familiar with the program, so 
can you mail me (offlist) and example input file, and the CLI command 
to run it. That way I can test it too, and see if I can get to work. If 
so, I might make a fink package for it.


thanks,

- Koen.



From plaza at infobiogen.fr  Mon Sep 27 09:38:58 2004
From: plaza at infobiogen.fr (Jean-Marc Plaza)
Date: Mon, 27 Sep 2004 15:38:58 +0200
Subject: [EMBOSS] Emboss 2.9.0 and PNG driver
Message-ID: <20040927133858.GC729229@babbage.infobiogen.fr>

Hello,
i would like to get the PNG driver for emboss 2.9.0 .

I have installed all packages needed for png (zlib-1.2.1,jpeg-6b,libpng-1.2.7,
libpng-1.2.7,libpng-1.2.7,libiconv-1.8,gd-2.0.22,) in a new directory: 
/usr/local/bio/src/EMBOSS/png (compilation 64 bit)

Then I have installed EMBOSS 2.9.0 using --with-pngdriver=/usr/local/bio/src/EMBOSS/png
Now when I run a graphic command in EMBOSS the png diver
is not proposed:

Graph type [x11]: png
Devices allowed are:-
postscript
ps
hpgl
hp7470
hp7580
meta
colourps
cps
xwindows
x11
tektronics
tekt
tek4107t
tek
none
null
text
data
xterm
Error: Invalid XY graph value 'png'
----------------------------------------------------------------

In the config.log, there is something that looks wrong:
  $ ./configure --with-pngdriver=/usr/local/bio/src/EMBOSS/png --prefix=/usr/local/bio/src/EMBOSS --enable-shared=no --enable-static --enable-large --enable-64

## --------- ##
## Platform. ##
## --------- ##

hostname = babbage
uname -m = sun4u
uname -r = 5.9
uname -s = SunOS
uname -v = Generic_112233-12

/usr/bin/uname -p = sparc
/bin/uname -X     = System = SunOS
Node = babbage
Release = 5.9
KernelID = Generic_112233-12
Machine = sun4u
BusType = <unknown>
Serial = <unknown>
Users = <unknown>
OEM# = 0
Origin# = 1
NumCPU = 64

/bin/arch              = sun4
/usr/bin/arch -k       = sun4u
/usr/convex/getsysinfo = unknown
hostinfo               = unknown
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /usr/local/bio/lassap/bin
PATH: /usr/java/bin
PATH: /usr/pkg/bin
PATH: /usr/pkg/sbin
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /usr/sbin
PATH: /usr/openwin/bin
PATH: /usr/dt/bin
PATH: /usr/X11R6/bin
PATH: /opt/SUNWspro/bin
PATH: /usr/ccs/bin
PATH: /usr/local/bio/bin

..

configure:23624: checking if png driver is wanted
configure:23631: result: yes
configure:23667: checking for inflateEnd in -lz
configure:23697: cc -o conftest   -O -xtarget=ultra -xarch=v9 -D__EXTENSIONS__ -I/usr/openwin/include -I/usr/local/include -DBENDIAN -I/u
/EMBOSS/png/include -L/usr/openwin/lib/sparcv9 -R/usr/openwin/lib/sparcv9 -L/usr/local/lib -R/usr/local/lib -L/usr/local/bio/src/EMBOSS/p
c -lz -L/usr/local/bio/src/EMBOSS/png/lib -lz -lm  -lnsl -lsocket >&5
configure:23703: $? = 0
configure:23707: test -z 
                         || test ! -s conftest.err
configure:23710: $? = 0
configure:23713: test -s conftest
configure:23716: $? = 0
configure:23729: result: yes
configure:23743: checking for png_destroy_read_struct in -lpng
configure:23773: cc -o conftest   -O -xtarget=ultra -xarch=v9 -D__EXTENSIONS__ -I/usr/openwin/include -I/usr/local/include -DBENDIAN -I/u
/EMBOSS/png/include -L/usr/openwin/lib/sparcv9 -R/usr/openwin/lib/sparcv9 -L/usr/local/lib -R/usr/local/lib -L/usr/local/bio/src/EMBOSS/p
c -lpng -L/usr/local/bio/src/EMBOSS/png/lib -lz -lm  -lnsl -lsocket >&5
configure:23779: $? = 0
configure:23783: test -z 
                         || test ! -s conftest.err
configure:23786: $? = 0
configure:23789: test -s conftest
configure:23792: $? = 0
configure:23805: result: yes
configure:23819: checking for gdImageCreateFromPng in -lgd
configure:23849: cc -o conftest   -O -xtarget=ultra -xarch=v9 -D__EXTENSIONS__ -I/usr/openwin/include -I/usr/local/include -DBENDIAN -I/u
/EMBOSS/png/include -L/usr/openwin/lib/sparcv9 -R/usr/openwin/lib/sparcv9 -L/usr/local/lib -R/usr/local/lib -L/usr/local/bio/src/EMBOSS/p
c -lgd -L/usr/local/bio/src/EMBOSS/png/lib -lgd -lpng -lz -lm -lm  -lnsl -lsocket >&5
Undefined                       first referenced
 symbol                             in file
libiconv_close                      /usr/local/bio/src/EMBOSS/png/lib/libgd.so
libiconv_open                       /usr/local/bio/src/EMBOSS/png/lib/libgd.so
libiconv                            /usr/local/bio/src/EMBOSS/png/lib/libgd.so
ld: fatal: Symbol referencing errors. No output written to conftest
configure:23855: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "EMBOSS"
| #define VERSION "2.9.0"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #ifdef __cplusplus
| extern "C" void exit (int);
| #endif
| #define HAVE_DIRENT_H 1
| #define STDC_HEADERS 1
| #define HAVE_UNISTD_H 1
| #define GETPGRP_VOID 1
| #define HAVE_STRFTIME 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FORK 1
| #define HAVE_VFORK 1
| #define HAVE_WORKING_VFORK 1
| #define HAVE_WORKING_FORK 1
| #define HAVE_VPRINTF 1
| #define HAVE_DOPRNT 1
| #define HAVE_MEMMOVE 1
| #define HAVE_LIBM 1
| /* end confdefs.h.  */
| 
| /* Override any gcc2 internal prototype to avoid an error.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| /* We use char because int might match the return type of a gcc2
|    builtin and then its argument prototype would still apply.  */
| char gdImageCreateFromPng ();
| int
| main ()
| {
| gdImageCreateFromPng ();
|   ;
|   return 0;
| }
configure:23881: result: no

----------------------------------------------------------

bash-2.05b$ file /usr/local/bio/src/EMBOSS/png/lib/libiconv.so
/usr/local/bio/src/EMBOSS/png/lib/libiconv.so:  ELF 64-bit MSB dynamic lib SPARCV9 Version 1, dynamically linked, not stripped

The parameters for the configure are:
CPPFLAGS="-I/usr/openwin/include -I/usr/local/include" LDFLAGS="-L/usr/openwin/lib/sparcv9 -R/usr/openwin/lib/sparcv9 -L/usr/local/lib -R/usr/local/lib" ./configure --with-pngdriver=/usr/local/bio/src/EMBOSS/png --prefix=/usr/local/bio/src/EMBOSS --enable-shared=no --enable-static --enable-large --enable-64




Thanks for your help in advance,


Jean-Marc


bash-2.05b$ uname -a
SunOS babbage 5.9 Generic_112233-12 sun4u sparc SUNW,Sun-Fire-15000


-- 
---------------------------------------------------------------
Jean-Marc PLAZA                     e-mail: plaza at infobiogen.fr               
INFOBIOGEN 523, place des terrasses de l'agora 91034 EVRY CEDEX
FRANCE     tel: +33 (0)1 60 87 37 11  fax: +33 (0)1 60 87 37 99



From augereau at u540.montp.inserm.fr  Wed Sep 29 11:43:04 2004
From: augereau at u540.montp.inserm.fr (Patrick Augereau)
Date: Wed, 29 Sep 2004 17:43:04 +0200
Subject: [EMBOSS] building under cygwin
Message-ID: <415AD808.2000903@u540.montp.inserm.fr>

Hello,
I try to build EMBOSS 2.9.0 under the cygwin environment; I succeeded in
overcoming a previous block by asking for static code; but I get the
following message; although I configured --without-x, it says that it is
unable to find -lX11; what's missing ? To try to bypass that error, I
installed xorg, but the failling still occurs at the same step.
Does anybody have a suggestion ?
Thanks in advance.
------------------------------------------------
make[3]: Entering directory `/home/patrick/EMBOSS-2.9.0/emboss/data/PROSITE'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/patrick/EMBOSS-2.9.0/emboss/data/PROSITE'
make[3]: Entering directory `/home/patrick/EMBOSS-2.9.0/emboss/data'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/patrick/EMBOSS-2.9.0/emboss/data'
make[2]: Leaving directory `/home/patrick/EMBOSS-2.9.0/emboss/data'
make[2]: Entering directory `/home/patrick/EMBOSS-2.9.0/emboss'
if gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKA
GE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\"
-DVERSION=\"2.9.0\"
 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1
-DHAVE_STDLIB_H=1 -DH
AVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_S
TDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DX_DISPLAY_MISSING=1
-DHAVE_DIRENT
_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1
-DHAVE_STRFTIME=1 -DHAV
E_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1
-DHAVE_WORKING_
FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1  -I. -I.
-I../nucleus -I.
./ajax -I../plplot  -DLENDIAN -DNO_AUTH  -s  -O2 -MT aaindexextract.o
-MD -MP -M
F ".deps/aaindexextract.Tpo" -c -o aaindexextract.o aaindexextract.c; \
then mv -f ".deps/aaindexextract.Tpo" ".deps/aaindexextract.Po"; else rm
-f ".de
ps/aaindexextract.Tpo"; exit 1; fi
/bin/bash ../libtool --mode=link gcc  -s  -O2   -o aaindexextract.exe
aaindexex
tract.o ../nucleus/libnucleus.la ../ajax/libajax.la
../plplot/libplplot.la  -lm

mkdir .libs
gcc -s -O2 -o aaindexextract.exe aaindexextract.o
../nucleus/.libs/libnucleus.a
 -L/home/patrick/EMBOSS-2.9.0/plplot -L/home/patrick/EMBOSS-2.9.0/ajax
/home/pat
rick/EMBOSS-2.9.0/ajax/.libs/libajax.a ../ajax/.libs/libajax.a
/home/patrick/EMB
OSS-2.9.0/plplot/.libs/libplplot.a ../plplot/.libs/libplplot.a -lX11
-lgd -lpng
-lz
/usr/lib/gcc-lib/i686-pc-cygwin/3.3.3/../../../../i686-pc-cygwin/bin/ld:
cannot
find -lX11
collect2: ld returned 1 exit status
make[2]: *** [aaindexextract.exe] Error 1
make[2]: Leaving directory `/home/patrick/EMBOSS-2.9.0/emboss'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/patrick/EMBOSS-2.9.0/emboss'
make: *** [all-recursive] Error 1
----------------------------------------------------------------

-- 
Patrick Augereau
Inserm U540
tel: 33 (0)4 67 04 37 13
fax: 33 (0)4 67 54 05 98



From promos at global-submit.com  Fri Sep 24 10:33:27 2004
From: promos at global-submit.com (promos at global-submit.com)
Date: Fri, 24 Sep 2004 06:33:27 -0400
Subject: [EMBOSS] Special Ends Soon...
Message-ID: <200409241033.GAA10971@sg8.global-submit.com>

You are receiving this e-mail because you were added to
http://www.global-submit.com in the past. Here is the URL
that was submitted to our search engine database.
http://bioinfo.pbi.nrc.ca:8090/EMBOSS/index.html

Start your Christmas advertising now. Get
your banner viewed accross our network
of over 80,000 different web pages.
During the Early Bird Special when you 
order 1 million exposure, we will double
your account at no extra charge. This
special applies to accounts activated 
before October 31st.

For more information, please visit our web
site at http://www.bannerscape.com or
gove me a call at 1 819 571 4943, 24
hours a day 7 days a week,  for more 
information

Thank you and have a nice day,

William Hanks
http://william.global-submit.com
william at global-submit.com
Call 1 819 571 4943 at any time.





RMV MESSAGE ID : T837098R53791

If would like to be taken out of our database then please visit this web site.
http://www.global-submit.com/cgi-bin/clipout.cgi?T837098R53791



From kellert at ohsu.edu  Fri Sep  3 02:52:55 2004
From: kellert at ohsu.edu (Thomas J Keller)
Date: Thu, 2 Sep 2004 19:52:55 -0700
Subject: [EMBOSS] backtranseq with ambiguities
Message-ID: <5B16DE52-FD54-11D8-A523-0003930405E2@ohsu.edu>

Greetings,
Is there a way to back translate a protein sequence and get a family of 
DNA sequences representing the possible gene sequences?

Thanks,
Tom K.

Tom Keller, Ph.D.
http://www.ohsu.edu/research/core
kellert at ohsu.edu
503-494-2442
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From kellert at ohsu.edu  Fri Sep  3 21:30:56 2004
From: kellert at ohsu.edu (Thomas J Keller)
Date: Fri, 3 Sep 2004 14:30:56 -0700
Subject: [EMBOSS] withrefm and proto for rebaseextract
Message-ID: <8A920A60-FDF0-11D8-8B08-0003930405E2@ohsu.edu>

Greetings,
The files available at http://rebase.neb.com/rebase/rebase.f37.html 
which offers the EMBOSS format rebase files, don't look like the input 
files (withrefm and proto) shown in the documentation. Which is which?

Thanks,
Tom K.

Tom Keller, Ph.D.
http://www.ohsu.edu/research/core
kellert at ohsu.edu
503-494-2442
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From David.Bauer at SCHERING.DE  Mon Sep  6 05:29:06 2004
From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE)
Date: Mon, 6 Sep 2004 07:29:06 +0200
Subject: Antwort: [EMBOSS] withrefm and proto for rebaseextract
Message-ID: <OFE94D0453.C22C2DE8-ONC1256F07.001DA1F6-C1256F07.001E228D@schering.de>


Hi Tom,

you can find the withrefm and proto files on the ftp server:
ftp://ftp.neb.com/pub/rebase/
The program rebaseextract creates from the 2 input files the emboss format
files embossre.enz, .ref and .sup and places them in .../data/REBASE.
The 3 files in format 37 are already reformated, so you don't need to run
rebaseextract but just rename them and copy in the emboss data directory.

David.



                                                                                                                           
                      "Thomas J                                                                                            
                      Keller"                                                                                              
                      <kellert at ohsu.ed         An:      emboss at hgmp.mrc.ac.uk                                              
                      u>                       Kopie:                                                                      
                      Gesendet von:            Thema:   [EMBOSS] withrefm and proto for rebaseextract                      
                      owner-emboss at hgm                                                                                     
                      p.mrc.ac.uk                                                                                          
                                                                                                                           
                                                                                                                           
                      03.09.2004 23:30                                                                                     
                                                                                                                           
                                                                                                                           




Greetings,
The files available at http://rebase.neb.com/rebase/rebase.f37.html
which offers the EMBOSS format rebase files, don't look like the input
files (withrefm and proto) shown in the documentation. Which is which?

Thanks,
Tom K.

Tom Keller, Ph.D.
http://www.ohsu.edu/research/core
kellert at ohsu.edu
503-494-2442






From mad at biol.unlp.edu.ar  Wed Sep  8 13:57:45 2004
From: mad at biol.unlp.edu.ar (Martin Sarachu)
Date: Wed,  8 Sep 2004 10:57:45 -0300
Subject: [EMBOSS] wEMBOSS-1.2
Message-ID: <1094651865.413f0fd9bb538@nahuel.biol.unlp.edu.ar>

This is to announce the release of wEMBOSS version 1.2

Some of the improvements are:
- Upgraded for EMBOSS-2.9.0
- Improved handling of project results for better performance

wEMBOSS is available for downloading on the wEMBOSS Portal
http://www.wemboss.org or download it using this link
http://www.wemboss.org/Folder.2003-09-11.4050/Folder.2003-09-11.4318C/wEMBOSS-1.2.tar.gz
Please post all your comments, suggestions and problems on the wEMBOSS forums
available on the Portal.

Enjoy wEMBOSS! 

-- 
Mart?n Sarachu
msarachu at biol.unlp.edu.ar
EMBnet Argentina
http://www.ar.embnet.org


From bioinfovijayaraj at yahoo.com  Fri Sep 10 07:52:14 2004
From: bioinfovijayaraj at yahoo.com (vijayaraj nagarajan)
Date: Fri, 10 Sep 2004 00:52:14 -0700 (PDT)
Subject: [EMBOSS] user-profile-regarding
Message-ID: <20040910075214.68385.qmail@web53606.mail.yahoo.com>

hi friends

i created a user with default BASH shel.
i created another user with default CSH shel.
i have set the path of the PLPLOT_LIB in the
/etc/profile


now..the problem is ...i could execute the text based
emboss programs in both the user prompts.

But, when i try to save the output in PS or in PNG
format...(X based...), then i could do this only in
the user who has BASH by default. 
i get the error (set path error), when i run the same
program with the other user, whose default shel is
csh.

we have gcg wisconsin also running in the same server
and the user need csh . so, if i change the shell from
default to bash, after logging in...even then i
couldnt run the x based outputs.....

pls help me to solve this problem.
i need to run both gcg and emboss from the same user.

i couldnt also set the environment after logging in to
the users...as i get the command not found error..in
the users...but not with the root.

pls help.
thanks in advance.
regards
vijay


	
		
__________________________________
Do you Yahoo!?
New and Improved Yahoo! Mail - 100MB free storage!
http://promotions.yahoo.com/new_mail 


From smarkel at scitegic.com  Fri Sep 10 17:23:24 2004
From: smarkel at scitegic.com (Scott Markel)
Date: Fri, 10 Sep 2004 10:23:24 -0700
Subject: [EMBOSS] difficulty using databases and "water"
Message-ID: <4141E30C.7000207@scitegic.com>

I'm using 2.9.0, built in cygwin, running in Windows XP.
I'm having problems creating databases for use with "water".

I created a USA database using dbifasta.

133 > dbifasta -idformat idacc -directory /C/SandBox/EMBOSS -filenames NRDB_protein_10.* -dbname NRDB_protein_10 -release 1.0 -date "10/09/04" -fields acnum -fields des -fields seqvn
Index a fasta database

I edited ~/.embossrc to include the new database.

134 > cat ~/.embossrc
DB NRDB_protein_10 [
    type: P
    format: fasta
    method: emblcd
    fields: "id acc sv des"
    directory: /C/SandBox/EMBOSS
    indexdirectory: /C/SandBox/EMBOSS
    file: NRDB_protein_10.fa
]

showdb does the right thing.

135 > showdb
Displays information on the currently available databases
# Name        Type ID  Qry All Comment
# ====        ==== ==  === === =======
NRDB_protein_10 P    OK  OK  OK  -

seqret can access all of the database.

136 > seqret NRDB_protein_10:\* stdout
Reads and writes (returns) sequences
 >XP_357594.1 XP_357594.1 similar to KIAA0960 protein [Mus musculus]
MCFPGEEVDRQLCRDAIFPIPVACDAPCPKDCVLSAWSSWSSCSHTCSGKTTEGKQTRAR
<shows all 10 sequences just fine>

I can't seem to access an individual sequence.

137 > seqret NRDB_protein_10:XP_357594
Reads and writes (returns) sequences
Error: Unable to read sequence 'NRDB_protein_10:XP_357594'
Died: seqret terminated: Bad value for '-sequence' and no prompt

What I'm really trying to do is run "water", but I expect
my database problems are impacting that.

161 > water -asequence query.fa -bsequence NRDB_protein_10:\*
Smith-Waterman local alignment.

    EMBOSS An error in ajarr.c at line 1805:
Token missing

Any pointers to documentation or examples would be greatly
appreciated.

Scott

-- 
Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at scitegic.com
SciTegic Inc.                       mobile: +1 858 205 3653
9665 Chesapeake Drive, Suite 401    voice:  +1 858 279 8800, ext. 253
San Diego, CA 92123                 fax:    +1 858 279 8804
USA                                 web:    http://www.scitegic.com




From d.m.a.martin at dundee.ac.uk  Mon Sep 13 16:36:08 2004
From: d.m.a.martin at dundee.ac.uk (David Martin)
Date: Mon, 13 Sep 2004 17:36:08 +0100
Subject: [EMBOSS] Sorting errors with DBIFLAT
Message-ID: <s145da9c.080@IA-GEN-A2.dundee.ac.uk>

I have been trying to index swissprot with DBIFLAT. For most sequences
it seems to work just fine, but for my pet sequence it fails, being
unable to find the sequence.

The reason is that it is sorting the list of IDs incorrectly before
writing them to entrynam.idx.

I wrote a short script to asciiify the entrynam.idx file and found the
appropriate entries.

Here is the excerpt:

ENTRY 1775562 :TFH3_HUMAN:475273634:0:1
ENTRY 1775563 :TFH3_MOUSE:475279037:0:1
ENTRY 1775564 :TFH4_HUMAN:475283197:0:1
ENTRY 1775565 :TFH4_MOUSE:475288725:0:1
ENTRY 1775566 :TFH4_PANTR:475293031:0:1
ENTRY 1775567 :TF_HUMAN:475515366:0:1
ENTRY 1775568 :TFL1_ARATH:475296099:0:1
ENTRY 1775569 :TF_MOUSE:475525712:0:1
ENTRY 1775570 :TFOX_HAEIN:475300602:0:1
ENTRY 1775571 :TFP2_HUMAN:475304815:0:1
ENTRY 1775572 :TFP2_MOUSE:475312007:0:1

This is most definitely not alphabetical order.

Any ideas on why/wherefor and fixes?

..d


From ableasby at hgmp.mrc.ac.uk  Mon Sep 13 18:05:27 2004
From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby)
Date: Mon, 13 Sep 2004 19:05:27 +0100 (BST)
Subject: [EMBOSS] Sorting errors with DBIFLAT
Message-ID: <200409131805.i8DI5RgU021092@bromine.hgmp.mrc.ac.uk>

This has just come up on emboss-bug and is a locale
feature (usually with GNU 'sort'). The solution
is to:
     setenv LC_ALL C

It has been known about for years. I expect we ought to put
it in the FAQ but it will become redundant when the new
indexing system is finished.

Alan


From Paul.Baumgartner at unibas.ch  Tue Sep 14 13:04:10 2004
From: Paul.Baumgartner at unibas.ch (Paul Baumgartner)
Date: Tue, 14 Sep 2004 15:04:10 +0200
Subject: [EMBOSS] primer3_core
Message-ID: <91E400FC-064E-11D9-8561-003065B9531E@unibas.ch>

Dear all

to generate primer3_core from primer3_1.0.0.tar archive the compiler 
generates the following Error:

  gcc -g -o primer3_core primer3_main.o oligotm.o dpal_primer.o 
format_output.o boulder_input.o '-static' -lm
ld: can't locate file for: -lcrt0.o
make: *** [primer3_core] Error 1

what could be wrong ?

( Mac OS 10.3.5 gcc 3.3)

thanks   Paul

Biozentrum
Paul Baumgartner
Zellbiologie
Klingelbergstrasse 70
CH-4056 Basel



From augereau at u540.montp.inserm.fr  Tue Sep 14 14:45:00 2004
From: augereau at u540.montp.inserm.fr (Patrick Augereau)
Date: Tue, 14 Sep 2004 16:45:00 +0200
Subject: [EMBOSS] building Emboss under cygwin
Message-ID: <414703EC.4030109@u540.montp.inserm.fr>

Hello,
I tried to build Emboss package in a cygwin environment, but after a
while, I got the following messages:

Creating library file: .libs/libajax.dll.a
.libs/ajgraph.o(.text+0x16):ajgraph.c: undefined reference to `_c_plschr'
.libs/ajgraph.o(.text+0x20d):ajgraph.c: undefined reference to `_c_plinit'
.libs/ajgraph.o(.text+0x278):ajgraph.c: undefined reference to `_c_plssub'
.libs/ajgraph.o(.text+0x3ce):ajgraph.c: undefined reference to `_c_plvpor'
.libs/ajgraph.o(.text+0x41b):ajgraph.c: undefined reference to `_c_plvsta'
.libs/ajgraph.o(.text+0x60b):ajgraph.c: undefined reference to `_c_pljoin'
.libs/ajgraph.o(.text+0x6d4):ajgraph.c: undefined reference to `_c_pljoin'
.libs/ajgraph.o(.text+0x963):ajgraph.c: undefined reference to `_c_plend'
.libs/ajgraph.o(.text+0xa99):ajgraph.c: undefined reference to `_c_plschr'
.libs/ajgraph.o(.text+0xaf4):ajgraph.c: undefined reference to `_c_plmtex'
.libs/ajgraph.o(.text+0xb25):ajgraph.c: undefined reference to `_c_plmtex'
.libs/ajgraph.o(.text+0xb56):ajgraph.c: undefined reference to `_c_plmtex'
.libs/ajgraph.o(.text+0xbb0):ajgraph.c: undefined reference to `_c_plmtex'
.libs/ajgraph.o(.text+0xf5e):ajgraph.c: undefined reference to `_c_plmtex'
.libs/ajgraph.o(.text+0x1fb6):ajgraph.c: undefined reference to `_c_plgpage'
.libs/ajgraph.o(.text+0x21a0):ajgraph.c: undefined reference to `_c_plbox'
.libs/ajgraph.o(.text+0x5bd1):ajgraph.c: undefined reference to `_c_plxswin'
.libs/ajgraph.o(.text+0x5c37):ajgraph.c: undefined reference to `_c_plxswin'
.libs/ajgraph.o(.text+0x6aee):ajgraph.c: undefined reference to
`_c_plfileinfo'
.libs/ajgraph.o(.text+0x3d):ajgraph.c: undefined reference to `_c_plstrlW'
.libs/ajgraph.o(.text+0x72):ajgraph.c: undefined reference to `_c_plgchrW'
.libs/ajgraph.o(.text+0xec):ajgraph.c: undefined reference to `_c_plsdev'
.libs/ajgraph.o(.text+0x1bc):ajgraph.c: undefined reference to `_c_plxsfnam'
.libs/ajgraph.o(.text+0x246):ajgraph.c: undefined reference to `_c_pladv'
.libs/ajgraph.o(.text+0x2ef):ajgraph.c: undefined reference to `_c_plwind'
.libs/ajgraph.o(.text+0x4f9):ajgraph.c: undefined reference to `_c_plline'
.libs/ajgraph.o(.text+0x75e):ajgraph.c: undefined reference to `_c_plfill'
.libs/ajgraph.o(.text+0x7d6):ajgraph.c: undefined reference to `_c_plscol0'
.libs/ajgraph.o(.text+0x84a):ajgraph.c: undefined reference to `_c_plpoin'
.libs/ajgraph.o(.text+0x9ff):ajgraph.c: undefined reference to `_c_plptex'
.libs/ajgraph.o(.text+0xa36):ajgraph.c: undefined reference to `_c_pllsty'
.libs/ajgraph.o(.text+0xa66):ajgraph.c: undefined reference to `_c_plpsty'
.libs/ajgraph.o(.text+0xbf6):ajgraph.c: undefined reference to `_c_plcol0'
.libs/ajgraph.o(.text+0xc3b):ajgraph.c: undefined reference to `_c_plwid'
.libs/ajgraph.o(.text+0x123b):ajgraph.c: undefined reference to
`_c_plxtrace'
.libs/ajgraph.o(.text+0x1f20):ajgraph.c: undefined reference to `_c_plgchr'
.libs/ajgraph.o(.text+0x2026):ajgraph.c: undefined reference to `_c_plsori'
.libs/ajgraph.o(.text+0x266e):ajgraph.c: undefined reference to `_c_pljoin'
.libs/ajgraph.o(.text+0x2ad4):ajgraph.c: undefined reference to `_c_plerry'
.libs/ajgraph.o(.text+0x2b64):ajgraph.c: undefined reference to `_c_plerrx'
collect2: ld returned 1 exit status
make[1]: *** [libajax.la] Error 1
make: *** [all-recursive] Error 1

What is missing in my cygwin install ? I tried to build under linux, and
all went fine, but with cygwin I always failed, whatever package I had
to the environment.
Thanks in advance for any help.

-- 
Patrick Augereau
Inserm U540
tel: 33 (0)4 67 04 37 13
fax: 33 (0)4 67 54 05 98


From ableasby at hgmp.mrc.ac.uk  Tue Sep 14 15:25:59 2004
From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby)
Date: Tue, 14 Sep 2004 16:25:59 +0100 (BST)
Subject: [EMBOSS] building Emboss under cygwin
Message-ID: <200409141525.i8EFPx3f029112@bromine.hgmp.mrc.ac.uk>

Others may be able to give more specific help regarding
individual packages that may need updating. If you
completely delete cygwin and reinstall the latest version
then it will work. The errors refer to changes made to
both cygwin and EMBOSS to enable production of shared
libraries on that system. If you want to experiment I'd
look in the gcc/ld(bintools)/make area.

HTH

Alan Bleasby


From Paul.Baumgartner at unibas.ch  Tue Sep 14 16:30:08 2004
From: Paul.Baumgartner at unibas.ch (Paul Baumgartner)
Date: Tue, 14 Sep 2004 18:30:08 +0200
Subject: [EMBOSS] primer3_core
In-Reply-To: <812BE26A-0661-11D9-B741-000393C44276@cgt.mc.duke.edu>
References: <91E400FC-064E-11D9-8561-003065B9531E@unibas.ch> <812BE26A-0661-11D9-B741-000393C44276@cgt.mc.duke.edu>
Message-ID: <575D1B6C-066B-11D9-8561-003065B9531E@unibas.ch>

I removed (#LIBOPTS ='-static') from the Makefile and the compiler 
generated primer3_core, cp to /sw/bin and run eprimer3 :
works for stdout
but outputfiles :
Output file [hsfau.eprimer3]:
Error: Unable to open file 'hsfau.eprimer3' for output
Output file [hsfau.eprimer3]: prim.txt
Error: Unable to open file 'prim.txt' for output
Died: eprimer3 terminated: Bad value for '-outfile' and no more retries

what commands are used for fink (the archive primer3_1.0.0.tar I have 
here)?

I installed emboss 2.8.0 by fink commander, but it seems that the 
component primer3_core is missing

thanks



On 14.09.2004, at 17:19, Jason Stajich wrote:

> Try removing the the '-static' from the makefile.
>
> This is final stmt to build primer3_core that works for me on OSX.
>
> gcc  -o primer3_core primer3_main.o oligotm.o dpal_primer.o 
> format_output.o boulder_input.o  -lm
>
> fink can build primer3 just fine so you may try that. There is also a 
> fink emboss pkg too.
> -jason
>
> On Sep 14, 2004, at 9:04 AM, Paul Baumgartner wrote:
>
>> locate file for: -lcrt0.o
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>
>
Biozentrum
Paul Baumgartner
Zellbiologie
Klingelbergstrasse 70
CH-4056 Basel



From kvddrift at earthlink.net  Tue Sep 14 22:39:46 2004
From: kvddrift at earthlink.net (Koen van der Drift)
Date: Tue, 14 Sep 2004 18:39:46 -0400
Subject: [EMBOSS] primer3_core
In-Reply-To: <575D1B6C-066B-11D9-8561-003065B9531E@unibas.ch>
References: <91E400FC-064E-11D9-8561-003065B9531E@unibas.ch> <812BE26A-0661-11D9-B741-000393C44276@cgt.mc.duke.edu> <575D1B6C-066B-11D9-8561-003065B9531E@unibas.ch>
Message-ID: <FA714CB8-069E-11D9-A857-003065A5FDCC@earthlink.net>


On Sep 14, 2004, at 12:30 PM, Paul Baumgartner wrote:

> I removed (#LIBOPTS ='-static') from the Makefile and the compiler 
> generated primer3_core, cp to /sw/bin and run eprimer3 :
> works for stdout
> but outputfiles :
> Output file [hsfau.eprimer3]:
> Error: Unable to open file 'hsfau.eprimer3' for output
> Output file [hsfau.eprimer3]: prim.txt
> Error: Unable to open file 'prim.txt' for output
> Died: eprimer3 terminated: Bad value for '-outfile' and no more retries
>
> what commands are used for fink (the archive primer3_1.0.0.tar I have 
> here)?
>
> I installed emboss 2.8.0 by fink commander, but it seems that the 
> component primer3_core is missing

Paul,

Primer3 is not present in fink right now. And as you can read in the 
eprimer3 docs it needs to be installed separately, so it not missing 
from the emboss package.

The above errors indicate a privileges problem, I suspect because you 
copied primer_core into /sw/lib. Remove it from /sw/bin and put it in 
/usr/local/bin, and try again. I am not familiar with the program, so 
can you mail me (offlist) and example input file, and the CLI command 
to run it. That way I can test it too, and see if I can get to work. If 
so, I might make a fink package for it.


thanks,

- Koen.



From plaza at infobiogen.fr  Mon Sep 27 13:38:58 2004
From: plaza at infobiogen.fr (Jean-Marc Plaza)
Date: Mon, 27 Sep 2004 15:38:58 +0200
Subject: [EMBOSS] Emboss 2.9.0 and PNG driver
Message-ID: <20040927133858.GC729229@babbage.infobiogen.fr>

Hello,
i would like to get the PNG driver for emboss 2.9.0 .

I have installed all packages needed for png (zlib-1.2.1,jpeg-6b,libpng-1.2.7,
libpng-1.2.7,libpng-1.2.7,libiconv-1.8,gd-2.0.22,) in a new directory: 
/usr/local/bio/src/EMBOSS/png (compilation 64 bit)

Then I have installed EMBOSS 2.9.0 using --with-pngdriver=/usr/local/bio/src/EMBOSS/png
Now when I run a graphic command in EMBOSS the png diver
is not proposed:

Graph type [x11]: png
Devices allowed are:-
postscript
ps
hpgl
hp7470
hp7580
meta
colourps
cps
xwindows
x11
tektronics
tekt
tek4107t
tek
none
null
text
data
xterm
Error: Invalid XY graph value 'png'
----------------------------------------------------------------

In the config.log, there is something that looks wrong:
  $ ./configure --with-pngdriver=/usr/local/bio/src/EMBOSS/png --prefix=/usr/local/bio/src/EMBOSS --enable-shared=no --enable-static --enable-large --enable-64

## --------- ##
## Platform. ##
## --------- ##

hostname = babbage
uname -m = sun4u
uname -r = 5.9
uname -s = SunOS
uname -v = Generic_112233-12

/usr/bin/uname -p = sparc
/bin/uname -X     = System = SunOS
Node = babbage
Release = 5.9
KernelID = Generic_112233-12
Machine = sun4u
BusType = <unknown>
Serial = <unknown>
Users = <unknown>
OEM# = 0
Origin# = 1
NumCPU = 64

/bin/arch              = sun4
/usr/bin/arch -k       = sun4u
/usr/convex/getsysinfo = unknown
hostinfo               = unknown
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /usr/local/bio/lassap/bin
PATH: /usr/java/bin
PATH: /usr/pkg/bin
PATH: /usr/pkg/sbin
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /usr/sbin
PATH: /usr/openwin/bin
PATH: /usr/dt/bin
PATH: /usr/X11R6/bin
PATH: /opt/SUNWspro/bin
PATH: /usr/ccs/bin
PATH: /usr/local/bio/bin

..

configure:23624: checking if png driver is wanted
configure:23631: result: yes
configure:23667: checking for inflateEnd in -lz
configure:23697: cc -o conftest   -O -xtarget=ultra -xarch=v9 -D__EXTENSIONS__ -I/usr/openwin/include -I/usr/local/include -DBENDIAN -I/u
/EMBOSS/png/include -L/usr/openwin/lib/sparcv9 -R/usr/openwin/lib/sparcv9 -L/usr/local/lib -R/usr/local/lib -L/usr/local/bio/src/EMBOSS/p
c -lz -L/usr/local/bio/src/EMBOSS/png/lib -lz -lm  -lnsl -lsocket >&5
configure:23703: $? = 0
configure:23707: test -z 
                         || test ! -s conftest.err
configure:23710: $? = 0
configure:23713: test -s conftest
configure:23716: $? = 0
configure:23729: result: yes
configure:23743: checking for png_destroy_read_struct in -lpng
configure:23773: cc -o conftest   -O -xtarget=ultra -xarch=v9 -D__EXTENSIONS__ -I/usr/openwin/include -I/usr/local/include -DBENDIAN -I/u
/EMBOSS/png/include -L/usr/openwin/lib/sparcv9 -R/usr/openwin/lib/sparcv9 -L/usr/local/lib -R/usr/local/lib -L/usr/local/bio/src/EMBOSS/p
c -lpng -L/usr/local/bio/src/EMBOSS/png/lib -lz -lm  -lnsl -lsocket >&5
configure:23779: $? = 0
configure:23783: test -z 
                         || test ! -s conftest.err
configure:23786: $? = 0
configure:23789: test -s conftest
configure:23792: $? = 0
configure:23805: result: yes
configure:23819: checking for gdImageCreateFromPng in -lgd
configure:23849: cc -o conftest   -O -xtarget=ultra -xarch=v9 -D__EXTENSIONS__ -I/usr/openwin/include -I/usr/local/include -DBENDIAN -I/u
/EMBOSS/png/include -L/usr/openwin/lib/sparcv9 -R/usr/openwin/lib/sparcv9 -L/usr/local/lib -R/usr/local/lib -L/usr/local/bio/src/EMBOSS/p
c -lgd -L/usr/local/bio/src/EMBOSS/png/lib -lgd -lpng -lz -lm -lm  -lnsl -lsocket >&5
Undefined                       first referenced
 symbol                             in file
libiconv_close                      /usr/local/bio/src/EMBOSS/png/lib/libgd.so
libiconv_open                       /usr/local/bio/src/EMBOSS/png/lib/libgd.so
libiconv                            /usr/local/bio/src/EMBOSS/png/lib/libgd.so
ld: fatal: Symbol referencing errors. No output written to conftest
configure:23855: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "EMBOSS"
| #define VERSION "2.9.0"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #ifdef __cplusplus
| extern "C" void exit (int);
| #endif
| #define HAVE_DIRENT_H 1
| #define STDC_HEADERS 1
| #define HAVE_UNISTD_H 1
| #define GETPGRP_VOID 1
| #define HAVE_STRFTIME 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FORK 1
| #define HAVE_VFORK 1
| #define HAVE_WORKING_VFORK 1
| #define HAVE_WORKING_FORK 1
| #define HAVE_VPRINTF 1
| #define HAVE_DOPRNT 1
| #define HAVE_MEMMOVE 1
| #define HAVE_LIBM 1
| /* end confdefs.h.  */
| 
| /* Override any gcc2 internal prototype to avoid an error.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| /* We use char because int might match the return type of a gcc2
|    builtin and then its argument prototype would still apply.  */
| char gdImageCreateFromPng ();
| int
| main ()
| {
| gdImageCreateFromPng ();
|   ;
|   return 0;
| }
configure:23881: result: no

----------------------------------------------------------

bash-2.05b$ file /usr/local/bio/src/EMBOSS/png/lib/libiconv.so
/usr/local/bio/src/EMBOSS/png/lib/libiconv.so:  ELF 64-bit MSB dynamic lib SPARCV9 Version 1, dynamically linked, not stripped

The parameters for the configure are:
CPPFLAGS="-I/usr/openwin/include -I/usr/local/include" LDFLAGS="-L/usr/openwin/lib/sparcv9 -R/usr/openwin/lib/sparcv9 -L/usr/local/lib -R/usr/local/lib" ./configure --with-pngdriver=/usr/local/bio/src/EMBOSS/png --prefix=/usr/local/bio/src/EMBOSS --enable-shared=no --enable-static --enable-large --enable-64




Thanks for your help in advance,


Jean-Marc


bash-2.05b$ uname -a
SunOS babbage 5.9 Generic_112233-12 sun4u sparc SUNW,Sun-Fire-15000


-- 
---------------------------------------------------------------
Jean-Marc PLAZA                     e-mail: plaza at infobiogen.fr               
INFOBIOGEN 523, place des terrasses de l'agora 91034 EVRY CEDEX
FRANCE     tel: +33 (0)1 60 87 37 11  fax: +33 (0)1 60 87 37 99



From augereau at u540.montp.inserm.fr  Wed Sep 29 15:43:04 2004
From: augereau at u540.montp.inserm.fr (Patrick Augereau)
Date: Wed, 29 Sep 2004 17:43:04 +0200
Subject: [EMBOSS] building under cygwin
Message-ID: <415AD808.2000903@u540.montp.inserm.fr>

Hello,
I try to build EMBOSS 2.9.0 under the cygwin environment; I succeeded in
overcoming a previous block by asking for static code; but I get the
following message; although I configured --without-x, it says that it is
unable to find -lX11; what's missing ? To try to bypass that error, I
installed xorg, but the failling still occurs at the same step.
Does anybody have a suggestion ?
Thanks in advance.
------------------------------------------------
make[3]: Entering directory `/home/patrick/EMBOSS-2.9.0/emboss/data/PROSITE'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/patrick/EMBOSS-2.9.0/emboss/data/PROSITE'
make[3]: Entering directory `/home/patrick/EMBOSS-2.9.0/emboss/data'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/patrick/EMBOSS-2.9.0/emboss/data'
make[2]: Leaving directory `/home/patrick/EMBOSS-2.9.0/emboss/data'
make[2]: Entering directory `/home/patrick/EMBOSS-2.9.0/emboss'
if gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKA
GE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\"
-DVERSION=\"2.9.0\"
 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1
-DHAVE_STDLIB_H=1 -DH
AVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_S
TDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DX_DISPLAY_MISSING=1
-DHAVE_DIRENT
_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1
-DHAVE_STRFTIME=1 -DHAV
E_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1
-DHAVE_WORKING_
FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1  -I. -I.
-I../nucleus -I.
./ajax -I../plplot  -DLENDIAN -DNO_AUTH  -s  -O2 -MT aaindexextract.o
-MD -MP -M
F ".deps/aaindexextract.Tpo" -c -o aaindexextract.o aaindexextract.c; \
then mv -f ".deps/aaindexextract.Tpo" ".deps/aaindexextract.Po"; else rm
-f ".de
ps/aaindexextract.Tpo"; exit 1; fi
/bin/bash ../libtool --mode=link gcc  -s  -O2   -o aaindexextract.exe
aaindexex
tract.o ../nucleus/libnucleus.la ../ajax/libajax.la
../plplot/libplplot.la  -lm

mkdir .libs
gcc -s -O2 -o aaindexextract.exe aaindexextract.o
../nucleus/.libs/libnucleus.a
 -L/home/patrick/EMBOSS-2.9.0/plplot -L/home/patrick/EMBOSS-2.9.0/ajax
/home/pat
rick/EMBOSS-2.9.0/ajax/.libs/libajax.a ../ajax/.libs/libajax.a
/home/patrick/EMB
OSS-2.9.0/plplot/.libs/libplplot.a ../plplot/.libs/libplplot.a -lX11
-lgd -lpng
-lz
/usr/lib/gcc-lib/i686-pc-cygwin/3.3.3/../../../../i686-pc-cygwin/bin/ld:
cannot
find -lX11
collect2: ld returned 1 exit status
make[2]: *** [aaindexextract.exe] Error 1
make[2]: Leaving directory `/home/patrick/EMBOSS-2.9.0/emboss'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/patrick/EMBOSS-2.9.0/emboss'
make: *** [all-recursive] Error 1
----------------------------------------------------------------

-- 
Patrick Augereau
Inserm U540
tel: 33 (0)4 67 04 37 13
fax: 33 (0)4 67 54 05 98