From owner-acedb@hgmp.mrc.ac.uk Mon Oct 2 08:22:09 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 220F517AE2; Mon, 2 Oct 2000 08:22:09 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id EB21E17ADF; Mon, 2 Oct 2000 08:22:07 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id C335317AFF; Fri, 29 Sep 2000 09:49:51 +0100 (BST) Received: from dfw7-1.relay.mail.uu.net (dfw7-1.relay.mail.uu.net [199.171.54.106]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 642FD415DF for ; Fri, 29 Sep 2000 09:49:49 +0100 (BST) Received: from nottingham.ac.uk by dfw7sosrv11.alter.net with ESMTP (peer crosschecked as: pat.ccc.nottingham.ac.uk [128.243.40.194]) id QQjish03118 for ; Fri, 29 Sep 2000 08:49:47 GMT Received: from oyez.ccc.nottingham.ac.uk ([128.243.241.164] helo=news.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.13 #2) id 13evrH-0004ZN-00 for bionet-software-acedb@moderators.isc.org; Fri, 29 Sep 2000 09:49:32 +0100 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 13evrT-0005Jh-00; Fri, 29 Sep 2000 09:49:43 +0100 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: Re: x-rated acedb Organization: ACS, The University of Nottingham Message-ID: References: <200009271009.LAA13179@griffin.sanger.ac.uk> Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: oyez.ccc.nottingham.ac.uk 970217383 20439 128.243.116.150 (29 Sep 2000 08:49:43 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 29 Sep 2000 08:49:43 GMT X-Sender: keith@thale Date: Mon, 2 Oct 2000 08:22:07 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk On 27 Sep 2000, Richard Durbin wrote: > Given we do this, Keith will have to replace x by n (e.g. with a perl > script) before parsing into acedb. I think that is reasonable. That's what we've already done, though we are also trying to contact the people who gave us the sequences to confirm that by 'X' they really mean 'N' (they also had N's in their sequences though, so it's not very clear why they used 'X'). I guess it would be useful for any curators who are not so familiar with IUPAC codes for acedb to maybe suggest replacing X's with N's (where the only improper code is 'X')...or just return a list of acceptable IUPAC codes? Keith ~ Keith Bradnam - Developer, Arabidopsis Genome Resource (AGR) ~ Nottingham Arabidopsis Stock Centre - http://nasc.nott.ac.uk/ ~ University Park, University of Nottingham, NG7 2RD, UK ~ Tel: (0115) 951 3091 From owner-acedb@hgmp.mrc.ac.uk Mon Oct 2 16:44:29 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1840C17B0A; Mon, 2 Oct 2000 16:44:28 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 48AB017B04; Mon, 2 Oct 2000 16:44:27 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 4300317AF0; Mon, 2 Oct 2000 14:52:00 +0100 (BST) Received: from postfix1.free.fr (postfix1.free.fr [212.27.32.21]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id B1EF7415DC for ; Mon, 2 Oct 2000 14:51:58 +0100 (BST) Received: from nnrp4.proxad.net (nnrp4.proxad.net [212.27.32.27]) by postfix1.free.fr (Postfix) with ESMTP id 815532819D for ; Mon, 2 Oct 2000 15:51:53 +0200 (MEST) Received: from localhost (localhost [[UNIX: localhost]]) by nnrp4.proxad.net (8.9.3/8.9.3/Debian 8.9.3-21) id PAA19287; Mon, 2 Oct 2000 15:51:53 +0200 To: bionet-software-acedb@net.bio.net Message-ID: <39D89406.C77D9568@marseille.inserm.fr> From: "F. Coulier" Organization: INSERM X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.11 i686) X-Accept-Language: fr-FR, en MIME-Version: 1.0 Newsgroups: bionet.software.acedb Subject: Pb starting gifaceserver Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Complaints-To: abuse@proxad.net X-Trace: nnrp4.proxad.net 970494713 195.220.67.155 (Mon, 02 Oct 2000 15:51:53 CEST) NNTP-Posting-Date: Mon, 02 Oct 2000 15:51:53 CEST Date: Mon, 2 Oct 2000 16:44:27 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Bonjour à tous, I am in the process of moving acedb to a new computer. I've (finally...) succeeded in installing acedb (4.7l) in /database/acedb, which runs ok. Now, I want to use Aceperl/Acebrowser. So, following what I've done for the "older" computer, I have: installed Aceperl 1.67 installed AceBrowser 2.10 (following its readme) got gifaceserver from acedb_server_4_7l_linux_libc6.tar.gz, moved it to /usr/local/bin, and made a symbolic link as follow: ln -s /usr/local/bin/gifaceserver /usr/local/bin/rpc.gifaceserver added the following line to /etc/services acedb 20000114/tcp added the following line to /etc/rpc acedb 20000114 rpc.gifaceserver added the following line to /etc/inetd.conf acedb/1 stream rpc/tcp wait acedb.U119 /usr/local/bin/rpc.gifaceserver rpc.gifaceserver /database/acedb 20000114 1200:1200:0 Restarted inetd But things don't behave as expected...and I can't access acedb on this new computer as I used to on the "older" one So, I've tried to start gifaceserver manually: $ gifaceserver /database/acedb 20000114 // Database directory: /database/acedb tar: Member names contain '..' Ne peut enregistrer le service: RPC: incapable d'effectuer la réception; errno = Connexion refusée unable to register (RPC_ACE, RPC_ACE_VERS, udp). Any suggestions on how to set things right will be appreciated! François -- François Coulier, mél: coulier@marseille.inserm.fr INSERM Unité 119, 27 bd Leï Roure, 13009 Marseille, France Tel: 33 (0) 4 91 26 04 26 (temporaire) Fax: 33 (0) 4 91 26 03 64 Site ouaibe: http://olan.marseille.inserm.fr/ From owner-acedb@hgmp.mrc.ac.uk Mon Oct 2 18:19:46 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id AA78517AD1; Mon, 2 Oct 2000 18:19:45 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 84DD517AC4; Mon, 2 Oct 2000 18:19:44 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 9AB5517AC4; Mon, 2 Oct 2000 18:19:21 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id D1795415DD for ; Mon, 2 Oct 2000 18:19:20 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA21901 for bionet-software-acedb@net.bio.net; Mon, 2 Oct 2000 18:19:20 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: Pb starting gifaceserver Organization: Sanger Centre Message-ID: <39D8C397.FC827C0A@sanger.ac.uk> References: <39D89406.C77D9568@marseille.inserm.fr> Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: niobium.hgmp.mrc.ac.uk 970507160 21899 193.60.84.177 (2 Oct 2000 17:19:20 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 2 Oct 2000 17:19:20 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Mon, 2 Oct 2000 18:19:44 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Francois, > tar: Member names contain '..' > Ne peut enregistrer le service: RPC: incapable d'effectuer la réception; > errno = Connexion refusée > unable to register (RPC_ACE, RPC_ACE_VERS, udp). === OK, something is very wrong, the above message suggests that for some reason the port is being opened using the udp protocol, not tcp. this may be because: 1) port 20000114 is already in use (look in /etc/services) 2) the operating system has decided that 20000114 is too large a number for the port and somehow "wrapped" the number round to a lower number which really is in use already. Try a port number between 1024 and 65535 that is not in /etc/services and see if that makes a difference. cheers Ed ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 Fax: +44 1223 494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Tue Oct 3 13:30:27 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 7590317B3C; Tue, 3 Oct 2000 13:30:26 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 8C15617A61; Tue, 3 Oct 2000 13:30:24 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id D910D17AF8; Tue, 3 Oct 2000 12:10:06 +0100 (BST) Received: from postfix1.free.fr (postfix1.free.fr [212.27.32.21]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id BF237415DA for ; Tue, 3 Oct 2000 12:10:05 +0100 (BST) Received: from nnrp1.proxad.net (nnrp1.proxad.net [212.27.32.75]) by postfix1.free.fr (Postfix) with ESMTP id 9F3D5281E2 for ; Tue, 3 Oct 2000 13:10:04 +0200 (MEST) Received: from localhost (localhost [[UNIX: localhost]]) by nnrp1.proxad.net (8.9.3/8.9.3/Debian 8.9.3-21) id NAA10901; Tue, 3 Oct 2000 13:09:59 +0200 To: bionet-software-acedb@net.bio.net Message-ID: <39D9BF9C.4C6A6CCD@marseille.inserm.fr> From: "F. Coulier" Organization: INSERM X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.11 i686) X-Accept-Language: fr-FR, en MIME-Version: 1.0 Newsgroups: bionet.software.acedb Subject: Re: Pb starting gifaceserver References: <39D89406.C77D9568@marseille.inserm.fr> <39D8C397.FC827C0A@sanger.ac.uk> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Complaints-To: abuse@proxad.net X-Trace: nnrp1.proxad.net 970571398 195.220.67.155 (Tue, 03 Oct 2000 13:09:58 MEST) NNTP-Posting-Date: Tue, 03 Oct 2000 13:09:58 MEST Date: Tue, 3 Oct 2000 13:30:24 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Ed Griffiths wrote: > > Francois, > > > tar: Member names contain '..' > > Ne peut enregistrer le service: RPC: incapable d'effectuer la réception; > > errno = Connexion refusée > > unable to register (RPC_ACE, RPC_ACE_VERS, udp). > === > OK, something is very wrong, the above message suggests that for some reason the > port is being opened using the udp protocol, not tcp. > > this may be because: > > 1) port 20000114 is already in use (look in /etc/services) > > 2) the operating system has decided that 20000114 is too large a number for the > port and somehow "wrapped" the number round to a lower number which really is in > use already. > > Try a port number between 1024 and 65535 that is not in /etc/services and see if > that makes a difference. > Thanks for your help, but... I've tried port 20114, I've checked it is not in /etc/services, I've edited /etc/rpc /etc/services and /etc/inetd.conf, tried to start gifaceserver manually, and got the same error message :=(( François -- François Coulier, mél: coulier@marseille.inserm.fr INSERM Unité 119, 27 bd Leï Roure, 13009 Marseille, France Tel: 33 (0) 4 91 26 04 26 (temporaire) Fax: 33 (0) 4 91 26 03 64 Site ouaibe: http://olan.marseille.inserm.fr/ From owner-acedb@hgmp.mrc.ac.uk Tue Oct 3 14:20:32 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 804AA17B3D; Tue, 3 Oct 2000 14:20:31 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 4229417A9C; Tue, 3 Oct 2000 14:20:30 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 3661C17A9C; Tue, 3 Oct 2000 13:33:18 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 22F2E415DF for ; Tue, 3 Oct 2000 13:33:17 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA14475 for bionet-software-acedb@net.bio.net; Tue, 3 Oct 2000 13:33:16 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: Pb starting gifaceserver Organization: Sanger Centre Message-ID: <39D9D20C.6975F7C5@sanger.ac.uk> References: <39D89406.C77D9568@marseille.inserm.fr> <39D8C397.FC827C0A@sanger.ac.uk> <39D9BF9C.4C6A6CCD@marseille.inserm.fr> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 970576396 14472 193.60.84.177 (3 Oct 2000 12:33:16 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 3 Oct 2000 12:33:16 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Tue, 3 Oct 2000 14:20:30 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Francois, Damn....ok, please could you either post here or send direct the following information: 1) output of 'uname -a' 2) your exact entries for /etc/services, /etc/rpc and /etc/inetd.conf 3) just double check which version of acedb you are using cheers Ed -- ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 Fax: +44 1223 494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Wed Oct 4 11:57:59 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8E82517AA7; Wed, 4 Oct 2000 11:57:58 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 0AC3F17AA2; Wed, 4 Oct 2000 11:57:56 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id B0F3C17A6A; Wed, 4 Oct 2000 11:47:17 +0100 (BST) Received: from sprettur.isnet.is (sprettur.isnet.is [193.4.58.19]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id D06A5415DE for ; Wed, 4 Oct 2000 11:47:14 +0100 (BST) Received: from nottingham.ac.uk (pat.ccc.nottingham.ac.uk [128.243.40.194]) by sprettur.isnet.is (8.11.0/8.11.0/isnet) with ESMTP id e94AlFA39997 for ; Wed, 4 Oct 2000 10:47:16 GMT (envelope-from news@oyez.ccc.nottingham.ac.uk) Received: from oyez.ccc.nottingham.ac.uk ([128.243.241.164] helo=news.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.13 #2) id 13gm4Y-0003EP-00 for bionet-software-acedb@moderators.isc.org; Wed, 04 Oct 2000 11:46:50 +0100 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 13gm4k-0005Dv-00; Wed, 4 Oct 2000 11:47:02 +0100 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: AceBrowser not displaying Locus information graphically Organization: ACS, The University of Nottingham Message-ID: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: oyez.ccc.nottingham.ac.uk 970656422 20081 128.243.116.150 (4 Oct 2000 10:47:02 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 4 Oct 2000 10:47:02 GMT X-Sender: keith@thale Date: Wed, 4 Oct 2000 11:57:56 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Just moved our database from our (aging) Sun machines to our new Compaq AlphaServer. Have just about managed to set up everything, but still a few glitches to iron out. In particular, I can no longer seem to view Locus objects as a a graphic (using the AceBroswer 'pic' script). The webpage returns the pic error gif which says: "The ACEDB server was unable to generate a picture of this object..." and the web error log reveals: [Wed Oct 4 09:06:26 2000] [error] Undefined subroutine CGI::Map Anyone encounter this? Is it some sort of problem with the pic script calling the CGI module? We have: acedb 4.7l Tru64 UNIX 5.0a perl 5.6.0 AceBrowser 2.10 AcePerl 1.62 CGI.pm 2.56 Keith ~ Keith Bradnam - Developer, Arabidopsis Genome Resource (AGR) ~ Nottingham Arabidopsis Stock Centre - http://nasc.nott.ac.uk/ ~ University Park, University of Nottingham, NG7 2RD, UK ~ Tel: (0115) 951 3091 From owner-acedb@hgmp.mrc.ac.uk Wed Oct 4 14:27:24 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4221E17AB5; Wed, 4 Oct 2000 14:27:23 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 54A0F17AA7; Wed, 4 Oct 2000 14:27:20 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 2B4BE17AF8; Wed, 4 Oct 2000 12:41:53 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Eric.Delorme@clermont.in2p3.fr (DELORME Eric) Newsgroups: bionet.software.acedb Subject: error of compilation with acedb Organization: LPC CNRS Message-ID: <39DB177C.91D1D54B@clermont.in2p3.fr> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 24C3417A76; Wed, 4 Oct 2000 12:41:50 +0100 (BST) X-Received: from clrhp04.in2p3.fr (clrhp04.in2p3.fr [193.48.80.80]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 9ACA1415DC for ; Wed, 4 Oct 2000 12:41:49 +0100 (BST) X-Received: from clermont.in2p3.fr (IDENT:delorme@clrpc138.in2p3.fr [193.48.80.24]) by clrhp04.in2p3.fr (8.9.3/8.9.3/In2p3) with ESMTP id NAA02607 for ; Wed, 4 Oct 2000 13:41:48 +0200 (METDST) X-Mailer: Mozilla 4.72 [fr] (X11; U; Linux 2.2.12-20 i686) X-Accept-Language: en X-To: acedb@net.bio.net Date: Wed, 4 Oct 2000 14:27:20 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hello Sorry for my english I have compiled ACEDB and i have some warning but when i compile defcpt.c i have the following error defcpt.c:85: initializer element is not constant make[1]: *** [defcpt.o] Error 1 make[1]: Leaving directory `/users_local1/bio/genome/prod_dev/annotation_v1/ACEDB/bin.LINUX_4_OPT' make: *** [xacembly] Error 2 can you help me ? thanks --- From owner-acedb@hgmp.mrc.ac.uk Wed Oct 4 14:52:29 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id A061A17AAF; Wed, 4 Oct 2000 14:52:28 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id BAEE217A83; Wed, 4 Oct 2000 14:52:26 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 3D53817B0A; Wed, 4 Oct 2000 14:36:28 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 8F4D8415DD for ; Wed, 4 Oct 2000 14:36:27 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA12123 for bionet-software-acedb@net.bio.net; Wed, 4 Oct 2000 14:36:27 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: error of compilation with acedb Organization: Sanger Centre Message-ID: <39DB325A.297E3CF2@sanger.ac.uk> References: <39DB177C.91D1D54B@clermont.in2p3.fr> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 970666587 12119 193.60.84.177 (4 Oct 2000 13:36:27 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 4 Oct 2000 13:36:27 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Wed, 4 Oct 2000 14:52:26 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Eric, > I have compiled ACEDB and i have some warning but when i compile > defcpt.c i have the following error > defcpt.c:85: initializer element is not constant > make[1]: *** [defcpt.o] Error 1 > make[1]: Leaving directory > `/users_local1/bio/genome/prod_dev/annotation_v1/ACEDB/bin.LINUX_4_OPT' > make: *** [xacembly] Error 2 Is this for acedb 4_7 or 4_8, what file did you download ? cheers Ed ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 Fax: +44 1223 494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Thu Oct 5 09:14:13 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 7B80917AC7; Thu, 5 Oct 2000 09:14:12 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 2262F17A5B; Thu, 5 Oct 2000 09:14:10 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id C4A1C17ABB; Wed, 4 Oct 2000 17:51:47 +0100 (BST) Received: from rutgers.rutgers.edu (bsd.rutgers.edu [165.230.4.71]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 18DA4415DD for ; Wed, 4 Oct 2000 17:51:46 +0100 (BST) Received: from nottingham.ac.uk (pat.ccc.nottingham.ac.uk [128.243.40.194]) by rutgers.rutgers.edu (8.8.8/8.8.8) with ESMTP id MAA00827 for ; Wed, 4 Oct 2000 12:51:44 -0400 (EDT) Received: from oyez.ccc.nottingham.ac.uk ([128.243.241.164] helo=news.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.13 #2) id 13grlM-00025M-00 for bionet-software-acedb@moderators.isc.org; Wed, 04 Oct 2000 17:51:24 +0100 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 13grld-0001Uk-00; Wed, 4 Oct 2000 17:51:41 +0100 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: Fault in gifaceserver? Organization: ACS, The University of Nottingham Message-ID: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: oyez.ccc.nottingham.ac.uk 970678301 5748 128.243.116.150 (4 Oct 2000 16:51:41 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 4 Oct 2000 16:51:41 GMT X-Sender: keith@thale Date: Thu, 5 Oct 2000 09:14:10 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk In order to try and pick apart my problem (see earlier post) I am trying to use aceclient to dump out a gif of a map in my database. When I use aceclient to access the database, it crashes/exits: % aceclient flora -port 50100 ERROR: failed to read file acedb@flora> gif display Map "Physical-I" ; gifdump abc //! Null answer - Error Code: 5 //! You may have timed out // Please report problems to mieg@kaa.crbm.cnrs-mop.fr //Bye This is on our new machine (running Tru64 UNIX). When I then try to access the same thing on an (almost identical) copy of the database on another machine (running Solaris), I get: % aceclient synteny -port 20001 acedb@synteny> gif display Map "Physical-I" ; gifdump abc // Reponse: 88 bytes. // GMAP Map "Physical-I" // I wrote the active graph to file abc // 0 Active Objects Both servers are running gifaceserver 4.7l. Does this imply that gifaceserver on our new (Tru64 UNIX) machine is faulty? Is there a better way of testing this? Any help appreciated. Keith ~ Keith Bradnam - Developer, Arabidopsis Genome Resource (AGR) ~ Nottingham Arabidopsis Stock Centre - http://nasc.nott.ac.uk/ ~ University Park, University of Nottingham, NG7 2RD, UK ~ Tel: (0115) 951 3091 From owner-acedb@hgmp.mrc.ac.uk Thu Oct 5 13:31:13 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 5722C17B84; Thu, 5 Oct 2000 13:31:13 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id D509017A7A; Thu, 5 Oct 2000 13:31:11 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 8090617BB5; Thu, 5 Oct 2000 10:43:51 +0100 (BST) Received: from sprettur.isnet.is (sprettur.isnet.is [193.4.58.19]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id A6A88415DD for ; Thu, 5 Oct 2000 10:43:40 +0100 (BST) Received: from nottingham.ac.uk (pat.ccc.nottingham.ac.uk [128.243.40.194]) by sprettur.isnet.is (8.11.0/8.11.0/isnet) with ESMTP id e959hhA34905 for ; Thu, 5 Oct 2000 09:43:43 GMT (envelope-from news@oyez.ccc.nottingham.ac.uk) Received: from oyez.ccc.nottingham.ac.uk ([128.243.241.164] helo=news.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.13 #2) id 13h7Ya-00034F-00 for bionet-software-acedb@moderators.isc.org; Thu, 05 Oct 2000 10:43:16 +0100 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 13h7Yt-0000Bd-00; Thu, 5 Oct 2000 10:43:35 +0100 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: CGI.pm problem Organization: ACS, The University of Nottingham Message-ID: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: oyez.ccc.nottingham.ac.uk 970739015 719 128.243.116.150 (5 Oct 2000 09:43:35 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 5 Oct 2000 09:43:35 GMT X-Sender: keith@thale Date: Thu, 5 Oct 2000 13:31:11 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk A potential warning... We upgraded CGI.pm to version 3.01 on our Tru64 machine and it seemed to stop our AceBrowser and WebAce interfaces from working. I've told Lincoln about this. Returning to CGI.pm 2.56 fixed the problems. Keith ~ Keith Bradnam - Developer, Arabidopsis Genome Resource (AGR) ~ Nottingham Arabidopsis Stock Centre - http://nasc.nott.ac.uk/ ~ University Park, University of Nottingham, NG7 2RD, UK ~ Tel: (0115) 951 3091 From owner-acedb@hgmp.mrc.ac.uk Thu Oct 5 13:31:19 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id BA54517B89; Thu, 5 Oct 2000 13:31:18 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 712C117B84; Thu, 5 Oct 2000 13:31:16 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 05A0717ADB; Thu, 5 Oct 2000 10:41:57 +0100 (BST) Received: from mailbox3.ucsd.edu (mailbox3.ucsd.edu [132.239.1.55]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 54333415D5 for ; Thu, 5 Oct 2000 10:41:50 +0100 (BST) Received: from nottingham.ac.uk (pat.ccc.nottingham.ac.uk [128.243.40.194]) by mailbox3.ucsd.edu (8.11.0/8.11.0) with ESMTP id e959flu01706 for ; Thu, 5 Oct 2000 02:41:48 -0700 (PDT) Received: from oyez.ccc.nottingham.ac.uk ([128.243.241.164] helo=news.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.13 #2) id 13h7Wm-0002zd-00 for bionet-software-acedb@moderators.isc.org; Thu, 05 Oct 2000 10:41:25 +0100 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 13h7X0-0000AT-00; Thu, 5 Oct 2000 10:41:38 +0100 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: gifaceserver fault (continued) Organization: ACS, The University of Nottingham Message-ID: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: oyez.ccc.nottingham.ac.uk 970738898 647 128.243.116.150 (5 Oct 2000 09:41:38 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 5 Oct 2000 09:41:38 GMT X-Sender: keith@thale Date: Thu, 5 Oct 2000 13:31:16 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi all, Following on from my previous posts, I am growing more convinced that there is some sort of problem with gifaceserver for the alpha platform. I should again state that this problem only manifests itself when trying to view very large maps (containing hundreds or thousands of objects). Trying to view any individual marker on one of these maps results in the same problem. To date, I have only been able to get this problem to occur in our AGR database, and not in any of the other 30 acedb databases we host on our server. The problem is that gifaceserver won't dump out the necessary image. This happens whether you access the database with WebAce, AceBrowser, or aceclient, but not xace (which is the bit that stumps me). In the first three cases, the graphic object does not appear. For AceBrowser the standard error gif is shown, for Webace the display defaults to the tree display and for aceclient, it falls over (see earlier post). This has happened on two separate Compaq Alphaservers running Tru64 UNIX, but doesn't happen on our older Sun workstations running Solaris (all with gifaceserver 4.7l) Any thoughts? Keith ~ Keith Bradnam - Developer, Arabidopsis Genome Resource (AGR) ~ Nottingham Arabidopsis Stock Centre - http://nasc.nott.ac.uk/ ~ University Park, University of Nottingham, NG7 2RD, UK ~ Tel: (0115) 951 3091 From owner-acedb@hgmp.mrc.ac.uk Thu Oct 12 11:40:25 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 916D917BD7; Thu, 12 Oct 2000 11:40:24 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 3509517BD3; Thu, 12 Oct 2000 11:40:23 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id D69E417BD4; Thu, 12 Oct 2000 11:39:49 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id A9A8B415D5 for ; Thu, 12 Oct 2000 11:39:48 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id LAA12132 for bionet-software-acedb@net.bio.net; Thu, 12 Oct 2000 11:39:48 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: error of compilation with acedb Organization: Sanger Centre Message-ID: <39E594F3.DFED597B@sanger.ac.uk> References: <39DB177C.91D1D54B@clermont.in2p3.fr> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 971347188 12130 193.60.84.177 (12 Oct 2000 10:39:48 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 12 Oct 2000 10:39:48 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Thu, 12 Oct 2000 11:40:23 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk > I have compiled ACEDB and i have some warning but when i compile > defcpt.c i have the following error > defcpt.c:85: initializer element is not constant This problem is now fixed, it occurs because on Linux 'stdin' and 'stderr' are defined to be the actual stdin/stderr file pointers and so are not constant, on other machines there is a per process struct that contains its own pointers to stdin/stderr, this struct is constant and so the compilation works on other machines. The code has been changed so it does not assume that stdin/stderr are constant. cheers Ed ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 Fax: +44 1223 494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Tue Oct 17 09:44:57 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D053717B35; Tue, 17 Oct 2000 09:44:55 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 16B5F17B35; Tue, 17 Oct 2000 09:44:53 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id B2ABA17A4E; Mon, 16 Oct 2000 15:28:12 +0100 (BST) Received: from postfix1.free.fr (postfix1.free.fr [212.27.32.21]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id AA08F415D5 for ; Mon, 16 Oct 2000 15:28:09 +0100 (BST) Received: from nnrp6.proxad.net (nnrp6.proxad.net [212.27.32.78]) by postfix1.free.fr (Postfix) with ESMTP id A6AE528128 for ; Mon, 16 Oct 2000 16:27:37 +0200 (MEST) Received: from localhost (localhost [[UNIX: localhost]]) by nnrp6.proxad.net (8.9.3/8.9.3/Debian 8.9.3-21) id QAA11539; Mon, 16 Oct 2000 16:27:37 +0200 To: bionet-software-acedb@net.bio.net Message-ID: <39EB10A2.9DE52D43@marseille.inserm.fr> From: F Coulier X-Mailer: Mozilla 4.73 [fr] (X11; I; Linux 2.2.15-4mdksecure i686) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.software.acedb Subject: Problems with gifaceserver/aceclient? Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Complaints-To: abuse@proxad.net X-Trace: nnrp6.proxad.net 971706457 195.220.67.166 (Mon, 16 Oct 2000 16:27:37 CEST) NNTP-Posting-Date: Mon, 16 Oct 2000 16:27:37 CEST Organization: Guest of ProXad - France Date: Tue, 17 Oct 2000 09:44:53 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Bonjour, Still trying to move Acedb from one computer to another..... Despite the help of Jean, Ed, Richard, and others, and after fixing a lot of things, including many mistakes on my part, I've still not been able to move ahead.... I can start gifaceserver at the command line: [fc@grun fc]$ /usr/bin/gifaceserver /database/acedb 20114 1200:1200:100 bash: /usr/bin/gifaceserver: Aucun fichier ou répertoire de ce type [ fc@grun fc]$ /usr/local/bin/gifaceserver /database/acedb 20114 1200:1200:100 // Database directory: /database/acedb tar: Member names contain `..' What does this "tar: Member names contain `..' " message means? Now, if I try to start aceclient : [fc@grun fc]$ /database/acedb/bin/aceclient 195.220.67.166 -port 20114 Erreur de segmentation What is this segmentation fault? If I try aceclient several time, I eventually get this (roughly once every 10 tries ) : [fc@grun fc]$ /database/acedb/bin/aceclient 195.220.67.166 -port 20114 ERROR: failed to read file acedb@195.220.67.166> What is this "ERROR: failed to read file" message? Despite this message, I can access acedb: acedb@195.220.67.166> find Author Brenner S // Reponse: 56 bytes. // Found 1 objects in this class // 1 Active Objects acedb@195.220.67.166> list // Reponse: 80 bytes. KeySet : Answer_1 Author: Brenner S // 1 object listed // 1 Active Objects acedb@195.220.67.166> Biblio // Reponse: 9788 bytes. Found 55 ref _1) [cgc30] The genetics of behaviour. Brenner S. British Medical Bulletin 29, 269-271 (1973) etc. for all of Brenner's references... My specific questions are: How can I get read of the error messages (actually, "how can I get rid of the cause of the error messages") What to do to have aceclient works every time. Any help will be greatly appreciated! François From owner-acedb@hgmp.mrc.ac.uk Tue Oct 17 10:01:43 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id A31CD17B6F; Tue, 17 Oct 2000 10:01:42 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 1CB3317B6D; Tue, 17 Oct 2000 10:01:39 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 1D6A517B2C; Tue, 17 Oct 2000 09:52:59 +0100 (BST) Received: from jess.sanger.ac.uk (jess.sanger.ac.uk [193.60.84.61]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 3FEF3415DD for ; Tue, 17 Oct 2000 09:52:58 +0100 (BST) Received: from griffin.sanger.ac.uk (root@griffin [193.60.84.177]) by jess.sanger.ac.uk (8.8.8/8.8.7) with ESMTP id JAA10772 for ; Tue, 17 Oct 2000 09:52:27 +0100 (BST) Received: from localhost (edgrif@localhost [127.0.0.1]) by griffin.sanger.ac.uk (8.8.7/8.8.7) with ESMTP id JAA19496 for ; Tue, 17 Oct 2000 09:44:29 +0100 (BST) From: Ed Griffiths To: acedb newsgroup on bionet Subject: question about Grid_show (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Newsgroups: bionet.software.acedb Date: Tue, 17 Oct 2000 10:01:39 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I have forwarded this for Jing Yu, please send any direct replies to him at: jingyu@dnalandmarks.ca not me !! Ed ---------- Forwarded message ---------- Date: Thu, 12 Oct 2000 16:29:59 -0400 From: Jing Yu To: acedb@sanger.ac.uk Subject: question about Grid_show Hello acedb newsletter group members, I hope here is the right place to send this mail, since I don't know anywhere else I may get the help. I got a problem when I recently tried to load my first "sample" Grid data. The .ace files are fine when they were read into ACEDB and the text information displays fine, but when I tried to open the grid display, I got message like this: Can't get Grid_display : "FATAL ERROR reported by program xace, in file graphxt.c at line 1051: text Bounds called on invalid graph type2". I don't know what's the problem and how to solve it. Could anyone give me help on that? For the convenience, a copy of the related ace file I used as my "sample" is attached as the following. Thank you for your help. Sincerely, Jing Yu from DNA LandMarks Canada ======================================================= Grid : BpcDNAII.1 Type 384_well Lines_at 3 4 Space_at 12 8 View GRID-1 Row 1 Clone DLM1 DLM2 DLM3 DLM4 DLM5 DLM6 DLM7 DLM8 DLM9 DLM10 DLM11 DLM12 DLM13 DLM14 DLM15 DLM16 DLM17 DLM18 DLM19 DLM20 DLM21 DLM22 DLM23 DLM24 Row 2 Clone DLM25 DLM26 DLM27 DLM28 DLM29 DLM30 DLM31 DLM32 DLM33 DLM34 DLM35 DLM36 DLM37 DLM38 DLM39 DLM40 DLM41 DLM42 DLM43 DLM44 DLM45 DLM46 DLM47 DLM48 Row 3 Clone DLM49 DLM50 DLM51 DLM52 DLM53 DLM54 DLM55 DLM56 DLM57 DLM58 DLM59 DLM60 DLM61 DLM62 DLM63 DLM64 DLM65 DLM66 DLM67 DLM68 DLM69 DLM70 DLM71 DLM72 Row 4 Clone DLM73 DLM74 DLM75 DLM76 DLM77 DLM78 DLM79 DLM80 DLM81 DLM82 DLM83 DLM84 DLM85 DLM86 DLM87 DLM88 DLM89 DLM90 DLM91 DLM92 DLM93 DLM94 DLM95 DLM96 Row 5 Clone DLM97 DLM98 DLM99 DLM100 DLM101 DLM102 DLM103 DLM104 DLM105 DLM106 DLM107 DLM108 DLM109 DLM110 DLM111 DLM112 DLM113 DLM114 DLM115 DLM116 DLM117 DLM118 DLM119 DLM120 Row 6 Clone DLM121 DLM122 DLM123 DLM124 DLM125 DLM126 DLM127 DLM128 DLM129 DLM130 DLM131 DLM132 DLM133 DLM134 DLM135 DLM136 DLM137 DLM138 DLM139 DLM140 DLM141 DLM142 DLM143 DLM144 Row 7 Clone DLM145 DLM146 DLM147 DLM148 DLM149 DLM150 DLM151 DLM152 DLM153 DLM154 DLM155 DLM156 DLM157 DLM158 DLM159 DLM160 DLM161 DLM162 DLM163 DLM164 DLM165 DLM166 DLM167 DLM168 Row 8 Clone DLM169 DLM170 DLM171 DLM172 DLM173 DLM174 DLM175 DLM176 DLM177 DLM178 DLM179 DLM180 DLM181 DLM182 DLM183 DLM184 DLM185 DLM186 DLM187 DLM188 DLM189 DLM190 DLM191 DLM192 Row 9 Clone DLM193 - DLM194 DLM195 DLM196 DLM197 DLM198 DLM199 DLM200 DLM201 DLM202 DLM203 DLM204 DLM205 DLM206 DLM207 DLM208 DLM209 DLM210 DLM211 DLM212 DLM213 DLM214 - Row 10 Clone DLM215 DLM216 DLM217 DLM218 DLM219 DLM220 DLM221 DLM222 DLM223 DLM224 DLM225 DLM226 DLM227 DLM228 DLM229 DLM230 DLM231 DLM232 DLM233 DLM234 DLM235 DLM236 DLM237 DLM238 Row 11 Clone DLM239 DLM240 DLM241 DLM242 DLM243 DLM244 DLM245 DLM246 DLM247 DLM248 DLM249 DLM250 DLM251 DLM252 DLM253 DLM254 DLM255 DLM256 DLM257 DLM258 DLM259 DLM260 DLM261 DLM262 Row 12 Clone DLM263 DLM264 DLM265 DLM266 DLM267 DLM268 DLM269 DLM270 DLM271 DLM272 DLM273 DLM274 DLM275 DLM276 DLM277 DLM278 DLM279 DLM280 DLM281 DLM282 DLM283 DLM284 DLM285 DLM286 Row 13 Clone DLM287 DLM288 DLM289 DLM290 DLM291 DLM292 DLM293 DLM294 DLM295 DLM296 DLM297 DLM298 DLM299 DLM300 - DLM301 DLM302 DLM303 DLM304 - DLM305 DLM306 DLM307 DLM308 Row 14 Clone DLM309 DLM310 DLM311 DLM312 DLM313 DLM314 DLM315 DLM316 DLM317 DLM318 DLM319 DLM320 DLM321 DLM322 DLM323 DLM324 DLM325 DLM326 DLM327 DLM328 DLM329 DLM330 DLM331 DLM332 Row 15 Clone DLM333 DLM334 DLM335 DLM336 DLM337 DLM338 DLM339 DLM340 DLM341 DLM342 DLM343 DLM344 DLM345 DLM346 DLM347 DLM348 DLM349 DLM350 DLM351 DLM352 DLM353 DLM354 DLM355 DLM356 Row 16 Clone DLM357 DLM358 DLM359 DLM360 DLM361 DLM362 DLM363 DLM364 DLM365 DLM366 DLM367 DLM368 DLM369 DLM370 DLM371 DLM372 DLM373 DLM374 DLM375 DLM376 - - - - View : "GRID-1" Grid_map 2 Colour BLUE Grid_map 2 Surround_colour GREEN Grid_map 2 Tag "Hybridizes_to" Grid_map 1 Colour LIGHTBLUE Grid_map 1 Surround_colour YELLOW Grid_map 1 Tag "Hybridizes_weak" Grid_edit_default "Hybridizes_to" Grid_edit_menu "Hybridizes_weak" Grid_edit_menu "Hybridizes_to" Clone : 1A1 Gridded BpcDNAII.1 Hybridizes_to 1A1 BpcDNAII.1 Hybridizes_weak 1AA1 BpcDNAII.1 Sequence DLM1.seq Clone : - Gridded BpcDNAII.1 Remark "empty well" Sequence : DLM1.seq DNA DLM1.seq 1168 DNA DLM1.seq GGATTCTCGTAATCACACTTCTC... (cut off the rest sequence in this mail) From owner-acedb@hgmp.mrc.ac.uk Tue Oct 17 10:02:23 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9751F17B44; Tue, 17 Oct 2000 10:02:22 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id EC20317B6F; Tue, 17 Oct 2000 10:02:20 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id CD17F17B35; Tue, 17 Oct 2000 09:47:26 +0100 (BST) Received: from jess.sanger.ac.uk (jess.sanger.ac.uk [193.60.84.61]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 1E494415DA for ; Tue, 17 Oct 2000 09:47:25 +0100 (BST) Received: from griffin.sanger.ac.uk (root@griffin [193.60.84.177]) by jess.sanger.ac.uk (8.8.8/8.8.7) with ESMTP id JAA09417 for ; Tue, 17 Oct 2000 09:47:24 +0100 (BST) Received: from localhost (edgrif@localhost [127.0.0.1]) by griffin.sanger.ac.uk (8.8.7/8.8.7) with ESMTP id JAA19495 for ; Tue, 17 Oct 2000 09:47:23 +0100 (BST) From: Ed Griffiths To: acedb newsgroup on bionet Subject: Re: question about Grid_show (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Newsgroups: bionet.software.acedb Date: Tue, 17 Oct 2000 10:02:20 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Forwarded from Jean... thye problem is in wspec/displays.wrm the grid display in you database is declared with the wrong type _DGRID -g TEXT_FULL_SCROLL -w 0.54 -height 0.78 -help Grid -m Grid is the coorect line to configure that display From owner-acedb@hgmp.mrc.ac.uk Thu Oct 19 10:24:18 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9661417BDF; Thu, 19 Oct 2000 10:24:17 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 27E2517BDC; Thu, 19 Oct 2000 10:24:16 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id C1F1417AB4; Thu, 19 Oct 2000 03:18:10 +0100 (BST) Received: from rutgers.rutgers.edu (rutgers.edu [165.230.4.76]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id DA23B415E3 for ; Thu, 19 Oct 2000 03:18:06 +0100 (BST) Received: from mss.rdc2.nsw.optushome.com.au (ha1.rdc2.nsw.optushome.com.au [203.164.2.50]) by rutgers.rutgers.edu (8.8.8/8.8.8) with ESMTP id WAA12825 for ; Wed, 18 Oct 2000 22:18:03 -0400 (EDT) Received: from news1.rochd1.qld.optushome.com.au ([203.164.20.213]) by mss.rdc2.nsw.optushome.com.au (InterMail vM.4.01.03.00 201-229-121) with ESMTP id <20001019021752.SPBC29783.mss.rdc2.nsw.optushome.com.au@news1.rochd1.qld.optushome.com.au> for ; Thu, 19 Oct 2000 13:17:52 +1100 Received: (from news@localhost) by news1.rochd1.qld.optushome.com.au (8.8.8+Sun/8.8.8) id NAA25960; Thu, 19 Oct 2000 13:17:51 +1100 (EST) To: bionet-software-acedb@moderators.isc.org From: "Smithy@Home" Newsgroups: bionet.software.acedb Subject: acedb and php4 X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Message-ID: X-Complaints-To: abuse@optushome.com.au X-Trace: news1.rochd1.qld.optushome.com.au 971921871 203.164.84.86 (Thu, 19 Oct 2000 13:17:51 EST) NNTP-Posting-Date: Thu, 19 Oct 2000 13:17:51 EST Organization: @Home Network Date: Thu, 19 Oct 2000 10:24:16 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk hey, Has anybody successfully used acedb with php4? thanks chez From owner-acedb@hgmp.mrc.ac.uk Thu Oct 19 13:01:59 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9FAE217B00; Thu, 19 Oct 2000 13:01:58 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 24FAA17AF9; Thu, 19 Oct 2000 13:01:57 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id CD83217A7F; Thu, 19 Oct 2000 11:59:40 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 0D8A8415E3 for ; Thu, 19 Oct 2000 11:59:40 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id LAA14633 for bionet-software-acedb@net.bio.net; Thu, 19 Oct 2000 11:59:39 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: Problems with gifaceserver/aceclient? Organization: Sanger Centre Message-ID: <39EED41A.8C282AEB@sanger.ac.uk> References: <39EB10A2.9DE52D43@marseille.inserm.fr> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 971953179 14631 193.60.84.177 (19 Oct 2000 10:59:39 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 19 Oct 2000 10:59:39 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Thu, 19 Oct 2000 13:01:57 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Francois, > tar: Member names contain `..' > > What does this "tar: Member names contain `..' " message means? Forget this message, its not significant, I'll do something about suppressing it at some time. > Now, if I try to start aceclient : > [fc@grun fc]$ /database/acedb/bin/aceclient 195.220.67.166 -port 20114 > Erreur de segmentation > > What is this segmentation fault? It's a serious program error, the program is trying to address memory that it is not allowed to have access to. > If I try aceclient several time, I eventually get this (roughly once > every 10 tries ) : This is _very_ surprising that it works at all given the above error. > [fc@grun fc]$ /database/acedb/bin/aceclient 195.220.67.166 -port 20114 > ERROR: failed to read file > acedb@195.220.67.166> > > What is this "ERROR: failed to read file" message? > Despite this message, I can access acedb: OK, what's happening is that the client manages to open one of the magic passwd files to get read/write access (see README about setting up the aceserver), but cannot read the contents of the file which is very strange. Please can you send me copies of your wspec/passwd.wrm, wspec/server.wrm and we'll take it from there. cheers Ed ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 Fax: +44 1223 494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Fri Oct 20 10:55:32 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D2D0317B32; Fri, 20 Oct 2000 10:55:31 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 0AA6E17B27; Fri, 20 Oct 2000 10:55:26 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 4A09A17AB1; Fri, 20 Oct 2000 07:33:55 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Eric.Delorme@clermont.in2p3.fr (DELORME Eric) Newsgroups: bionet.software.acedb Subject: Segmentation fault with a blast under Linux Red-Hat6.1 Organization: LPC CNRS Message-ID: <39EFE74B.99E83B8B@clermont.in2p3.fr> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 7C7D517B0C; Fri, 20 Oct 2000 07:33:53 +0100 (BST) X-Received: from clrhp04.in2p3.fr (clrhp04.in2p3.fr [193.48.80.80]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 3A502415E1 for ; Fri, 20 Oct 2000 07:33:49 +0100 (BST) X-Received: from clermont.in2p3.fr (IDENT:delorme@clrpc138.in2p3.fr [193.48.80.24]) by clrhp04.in2p3.fr (8.9.3/8.9.3/In2p3) with ESMTP id IAA06445 for ; Fri, 20 Oct 2000 08:33:48 +0200 (METDST) X-Mailer: Mozilla 4.72 [fr] (X11; U; Linux 2.2.12-20 i686) X-Accept-Language: en X-To: acedb@net.bio.net Date: Fri, 20 Oct 2000 10:55:26 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hello When i send a blast with ACEDB, i have the result who save but the application close with a message segmentation fault. Under sun there are no problem the application is stable. Under Linux Red-hat 6.1 the application is not stable . Do you have this problem ? thanks --- From owner-acedb@hgmp.mrc.ac.uk Tue Oct 31 16:20:49 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 489C017AF1; Tue, 31 Oct 2000 16:20:48 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 5878117AF5; Tue, 31 Oct 2000 16:20:40 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 9F30117B20; Sun, 29 Oct 2000 05:24:44 +0000 (GMT) Received: from mailbox1.ucsd.edu (mailbox1.ucsd.edu [132.239.1.53]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 7C965415D5 for ; Sun, 29 Oct 2000 05:24:39 +0000 (GMT) Received: from news3.bu.edu (NEWS3.BU.EDU [128.197.27.152]) by mailbox1.ucsd.edu (8.11.0/8.11.0) with ESMTP id e9T5OcP29487 for ; Sat, 28 Oct 2000 22:24:38 -0700 (PDT) Received: (from news@localhost) by news3.bu.edu ((8.9.3.buoit.v1.0)/8.9.3/(BU-S-10/28/1999-v1.0)) id BAA23355 for bionet-software-acedb@moderators.isc.org; Sun, 29 Oct 2000 01:24:37 -0400 (EDT) To: bionet-software-acedb@moderators.isc.org From: "Faramarz Valafar" Subject: METMBS'2001 Call for papers and technical sessions Organization: Boston University X-Trace: news3.bu.edu 972797077 23353 128.197.61.175 (29 Oct 2000 05:24:37 GMT) X-Complaints-To: news@bu.edu X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Newsgroups: bionet.software.acedb Message-Id: <20001031162040.5878117AF5@mercury.hgmp.mrc.ac.uk> Date: Tue, 31 Oct 2000 16:20:40 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk The 2001 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'2001) http://www.cns.bu.edu/metmbs/ June 25 - 28, 2001 Monte Carlo Resort, Las Vegas, Nevada, USA Call for Papers Recent advances in computer technology have provided the tools and the environment to study, analyze, and better understand complex systems. This technological development has enabled researchers to collect and analyze massive amounts of data to a scale previously not possible. The impact of this technology is now being felt in the medical field and in the biological sciences. In recent years, research in interdisciplinary areas such as Bioinformatics and computer assisted medical decision-making has dramatically intensified. METMBS'2001 aims to provide a platform for researchers to present and discuss recent breakthroughs in this area. The METMBS'2001 Conference will be held concurrently (i.e., same location and dates) with a number of international conferences: International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'2001), the International Conference on Imaging Science, Systems, and Technology (CISST'2001), International Conference on Internet computing (IC'2001), ... The last concurrent meeting of this group of conferences in year 2000 had research contributions from 46 countries (the events held in Las Vegas had over 1100 participants from all over the world.) It is hoped that METMBS'2001 will maintain its strong international flavor in this year's meeting as well. You are invited to submit a draft paper of about 4 pages and/or a proposal to organize a technical session (see below for submission information). All accepted papers will be published in the conference proceedings. THE NAMES OF TECHNICAL SESSION CHAIRS WILL APPEAR AS ASSOCIATE EDITORS ON THE COVER OF THE CONFERENCE PROCEEDINGS. SCOPE Topics of interest include, but are not limited to, the following: o Bioinformatics: This includes informatics techniques in genomics gene sequencing, gene pattern discovery, gene pattern-function studies, and other genomics related studies). o Data mining in medicine and biological sciences. o Pattern recognition in medicine and biological sciences. o Signal processing in medicine and biological sciences (e.g. biomedical signal processing, etc.) o Image processing in medicine and biological sciences (e.g. biomedical image processing, biomedical imaging, etc.) o Medical decision-making. o Medical Physics. o Biomedical Engineering. o Biomedical Electronics. o Biosignal interpretation. o Any application of computers in Medicine and biological sciences (protein structure-function analysis, drug and protein design, molecular modeling and simulation, etc.) o Application of information technology in biomedicine (e.g. medical database management, information retrieval and use of computers in hospitals) o Application of Computational Intelligence (artificial neural networks, fuzzy logic, and evolutionary computing) in medicine and biological sciences o Medical and bio-computing. o Computer-based medical systems (automation in medicine, etc.) o Recent history (1990-1999) of Mathematics and engineering techniques in medicine and biological sciences, and what to expect during the next decade (2000-2009); New horizons. Review articles) o Other aspects and applications relating to technological advancements in medicine and biological sciences. SUBMISSION OF PAPERS Prospective authors are invited to submit three copies of their draft paper (about 4 pages) to F. Valafar (address is given below) by March 1, 2001. E-mail and Fax submissions are also acceptable. The length of the Camera-Ready papers (if accepted) will be limited to 7 pages. Papers must not have been previously published or currently submitted for publication elsewhere. The first page of the draft paper should include: title of the paper, name, affiliation, postal address, E-mail address, telephone number, and Fax number for each author. The first page should also include the name of the author who will be presenting the paper (if accepted) and a maximum of 5 keywords. PROPOSAL FOR ORGANIZING TECHNICAL SESSIONS Each technical session will have at least 6 paper presentations. The session chairs will be responsible for all aspects of their sessions, including soliciting papers, reviewing, selecting, ... The names of session chairs will appear as Associate Editors in the conference proceedings. After the conference, some sessions will be considered for publication in appropriate journals as Special Issues with the session proposer as the Guest Editor of the journal. Proposals to organize technical sessions should include the following information: name and address (+ E-mail) of the proposer, title of session, a 100-word description of the topic of the session, and a short description on how the session will be advertised (in most cases, session proposers solicit papers from colleagues and researchers whose work is known to the session proposer). Mail your proposal to F. Valafar (address is given below); E-mail submissions are preferred. EVALUATION PROCESS Papers will be evaluated for originality, significance, clarity, and soundness. Two researchers in the topical area will referee each paper. The Camera-Ready papers will be reviewed by one person. PUBLICATION The conference proceedings will be published by CSREA Press (ISBN). The proceedings will be available at the conference. Some accepted papers will also be considered for journal publication (soon after the conference). ORGANIZERS/SPONSORS A number of university faculty members and their staff, in cooperation with the Monte Carlo Resort (Conference Division, Las Vegas), will be organizing the conference. The conference will be sponsored by Computer Science Research, Education, & Applications Press (CSREA: USA Federal EIN # 58-2171953) in cooperation with research centers, international associations, international research groups, and developers of high-performance machines and systems. The complete list of sponsors and co-sponsors will be available at a later time. The last conference's sponsors included: CSREA, the National Supercomputing Center for Energy and the Environment - DOE, The International Association for Mathematics and Computers in Simulation, The International Technology Institute (ITI), The Java High Performance Computing research group, World Scientific and Engineering Society, Sundance Digital Signal Processing Inc., the Computer Vision Research and Applications Tech., and more. LOCATION OF CONFERENCE The conference will be held in the Monte Carlo Resort Hotel, Las Vegas, Nevada, USA. This is a mega hotel with excellent conference facilities and over 3000 rooms. The hotel is minutes from the Las Vegas airport with free shuttles to and from the airport. This hotel has many vacation and recreational attractions, including: waterfalls, casino, spa, pools & kiddie pools, sunning decks, Easy River water ride, wave pool with cascades, lighted tennis courts, health spa (with workout equipment, whirlpool, sauna, ...), arcade virtual reality game rooms, nightly shows, snack bars, a number of restaurants, shopping area, bars, ... Many of these attractions are open 24 hours a day and most are suitable for families and children. The negotiated hotel's room rate for conference attendees is very reasonable ($79 + tax) per night (no extra charge for double occupancy) for the duration of the conference. The hotel is within walking distance from most other Las Vegas attractions (major shopping areas, recreational destinations, fine dining and night clubs, free street shows, and more). For the benefit of our international colleagues: the state of Nevada neighbors with the states of California, Oregon, Idaho, Utah, and Arizona. Las Vegas is only a few driving hours away from other major cities and attractions, including: Los Angeles, San Diego, Phoenix, the Grand Canyon, and more. EXHIBITION An exhibit is planned for the duration of the conference. We have reserved 20+ exhibit spaces. Interested parties should contact F. Valafar (address is given below). All exhibitors will be considered to be the co-sponsors of the conference. IMPORTANT DATES March 1, 2001 (Thursday): Draft papers (about 4 pages) due April 2, 2001 (Monday): Notification of acceptance May 1, 2001 (Tuesday): Camera-Ready papers & Prereg. due June 25 - 28, 2001: METMBS'2001 Conference Proposals to organize technical sessions should be submitted as soon as possible. All accepted papers are expected to be presented at the conference. MEMBERS OF PROGRAM & ORGANIZING COMMITTEES The Program Committee is currently being formed. Those interested in joining the Program Committee should e-mail F. Valafar (faramarz@cns.bu.edu) the following information: Name, affiliation and position, complete mailing address, e-mail address, tel/fax numbers, a short biography together with research interests. OTHER INFORMATION It is planned to add other related conferences and workshops to be held simultaneously (same location and dates) creating an international multiconference. Each conference will have it's own proceedings and technical/research sessions. CONFERENCE CONTACT: Faramarz Valafar Cognitive and Neural Systems Boston University 677 Beacon Street Boston, MA 02215 Tel: (617) 353-5134 Fax: (617) 353-7755 E-mail: Faramarz@cns.bu.edu