From ggibbs at hgmp.mrc.ac.uk Tue Jul 4 06:39:56 2000 From: ggibbs at hgmp.mrc.ac.uk (Geoff Gibbs) Date: Tue, 4 Jul 2000 11:39:56 +0100 (BST) Subject: test Message-ID: <20000704103956.BD049FAF4@gold.hgmp.mrc.ac.uk> Alan, just to test that the emboss list works and that you are on it. Geoff From ableasby at hgmp.mrc.ac.uk Sat Jul 15 18:29:33 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Sat, 15 Jul 2000 23:29:33 +0100 (BST) Subject: EMBOSS has moved to HGMP Message-ID: <200007152229.XAA19252@bromine.hgmp.mrc.ac.uk> Dear EMBOSS folk, Yes, EMBOSS has indeed moved. Please note the new address for the web pages. It is: http://www.uk.embnet.org/Software/EMBOSS or if you prefer http://www.hgmp.mrc.ac.uk/Software/EMBOSS they are the same address. Similarly the ftp server becomes: ftp://ftp.uk.embnet.org/pub/EMBOSS or ftp://ftp.hgmp.mrc.ac.uk/pub/EMBOSS Why the move? It is because Peter Rice and Ian Longden have both just gone into the commercial sector. Peter has gone to Lion and Ian to Informatica. This left noone at Sanger with the experience to maintain EMBOSS therefore it finds a welcome home with the HGMP developers. I surely speak for all of us when I thank Peter and Ian for their work... although Peter will still be active with EMBOSS from the Lion point of view so this is neither an obituary or E.J. Thribb poem. Both still have their Sanger usernames intact for now. And so on to the changes. You will notice a different look and feel to the web pages. This is in preparation for the imminent announcement of Release 1.0.0. You will see this reflected in the filename of EMBOSS on the ftp server. It is EMBOSS-1.0.0.tar.gz N.B: As of this distribution there is an extra 'emboss' directory level at the top. This is to allow the --prefix configuration option to (optionally) install directories there. The instructions for use of the CVS server have also changed. Please read the new instructions on the web pages if you use this method. This server also has the extra directory mentioned above. Also note that there is no alias for cvs.hgmp.mrc.ac.uk at the moment i.e. cvs.uk.embnet.org will not work but the former will. The mail list addresses have changed accordingly. They are: emboss at uk.embnet.org emboss-dev at uk.embnet.org or emboss at hgmp.mrc.ac.uk emboss-dev at hgmp.mrc.ac.uk All the subscription addresses have been moved over. The majordomo server at our site works in the same way as on the Sanger site. N.B.: Until the Sanger site change their links to redirect to HGMP their site is still active. It is not being updated though. To get the latest updates you must use the new addresses. I am bound to have forgotten something as we've all had to work like demons to move things over and get to a stage where we can advertise release 1.0.0. I will post if anything important springs to mind. Finally, it is St Swithins Day so, if the new service works today it will probably work for the next 40. If not you can always email: emboss-bug at uk.embnet.org or emboss-bug at hgmp.mrc.ac.uk Cheers Alan HGMP From ableasby at hgmp.mrc.ac.uk Sun Jul 16 07:07:23 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Sun, 16 Jul 2000 12:07:23 +0100 (BST) Subject: Directory Levels Message-ID: <200007161107.MAA00672@bromine.hgmp.mrc.ac.uk> I made a slight error in the move announcement. There is no extra emboss directory level in the ftp distribution but there is in the CVS distribution. Alan From David.Lapointe at umassmed.edu Wed Jul 19 16:49:35 2000 From: David.Lapointe at umassmed.edu (Lapointe, David) Date: Wed, 19 Jul 2000 16:49:35 -0400 Subject: Compile problem Message-ID: For some reason, configure --with-pngdriver=/usr/local/lib ( where the z,libpng, and gd libs are) refuses to configure png checking for gdImageCreateFromPng in -lgd... no need to upgrade gd for png driver for plplot No png driver will be made due to librarys missing/old Well, it's not missing and it's not old ( gd 1.8.3 ). This is an IRIX 6.5 system. David Lapointe, Ph.D. Research Computing Manager 6-5141 "Great minds think a lot" From starksb at ebi.ac.uk Thu Jul 20 02:00:55 2000 From: starksb at ebi.ac.uk (David Starks-Browning) Date: Thu, 20 Jul 2000 07:00:55 +0100 Subject: Compile problem In-Reply-To: References: Message-ID: <1800-Thu20Jul2000070055+0100-starksb@ebi.ac.uk> On Wednesday 19 Jul 00, Lapointe, David writes: > For some reason, configure --with-pngdriver=/usr/local/lib ( where the > z,libpng, and gd > libs are) refuses to configure png > > checking for gdImageCreateFromPng in -lgd... no > need to upgrade gd for png driver for plplot > No png driver will be made due to librarys missing/old > > Well, it's not missing and it's not old ( gd 1.8.3 ). > > This is an IRIX 6.5 system. Just guessing here, because you don't provide enough details, but could it be that EMBOSS, and any of the existing z, png or gd libs in /usr/local/lib have different ABIs? If you don't know what I mean ('man abi' is a good start), let me know and I'll try to help you get it sorted. Cheers, David ------------------------------------------------------------------- David Starks-Browning | starksb at ebi.ac.uk EMBL Outstation -- | The European Bioinformatics Institute | Wellcome Trust Genome Campus | tel: +44 (1223) 494 616 Hinxton, Cambridge, CB10 1SD, UK | fax: +44 (1223) 494 468 ------------------------------------------------------------------- From ptribble at hgmp.mrc.ac.uk Thu Jul 20 04:14:42 2000 From: ptribble at hgmp.mrc.ac.uk (Peter C. Tribble) Date: Thu, 20 Jul 2000 09:14:42 +0100 (BST) Subject: Compile problem Message-ID: <20000720081442.1CC6F415DA@mercury.hgmp.mrc.ac.uk> David Lapointe said: >>>For some reason, configure --with-pngdriver=/usr/local/lib ( where the >>>z,libpng, and gd >>>libs are) refuses to configure png >>> >>>checking for gdImageCreateFromPng in -lgd... no >>>need to upgrade gd for png driver for plplot >>>No png driver will be made due to librarys missing/old >>> >>>Well, it's not missing and it's not old ( gd 1.8.3 ). It's too new, I suspect. gd 1.8.3 requires jpeg as well as png, and emboss doesn't know that yet. You should be able to look at config.log to work out what's gone wrong, but currently emboss won't work with gd 1.8.3. (I spotted this last week on OpenBSD, which didn't generate any link errors and cheerfully built emboss, but then none of the binaries would actually run because they couldn't find any of the jpeg stuff at runtime.) -Peter Tribble HGMP Computing Services http://www.hgmp.mrc.ac.uk/~ptribble/ From bauer at genprofile.com Thu Jul 20 04:24:44 2000 From: bauer at genprofile.com (David Bauer) Date: Thu, 20 Jul 2000 10:24:44 +0200 Subject: Compile problem References: <20000720081442.1CC6F415DA@mercury.hgmp.mrc.ac.uk> Message-ID: <3976B74C.6FE522FF@genprofile.com> "Peter C. Tribble" wrote: > out what's gone wrong, but currently emboss won't work with gd 1.8.3. Yup, that's new to me. I'm running emboss on FreeBSD with exactly this version of gd and it can create png output without problems. -- Dr. David Bauer GenProfile AG, Max-Delbrueck-Center, Erwin-Negelein-Haus Robert-Roessle-Str. 10, D-13125 Berlin, Germany bauer at genprofile.com, Tel:49-30-94892165, FAX:49-30-94892151 From ableasby at hgmp.mrc.ac.uk Thu Jul 20 04:56:08 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Thu, 20 Jul 2000 09:56:08 +0100 (BST) Subject: Compile problem Message-ID: <200007200856.JAA24845@bromine.hgmp.mrc.ac.uk> It is certainly nothing to do with JPEG. That is a problem I'm investigating (I can't get EMBOSS to fail with 1.8.3 at the moment either.) The problem David was happening was, for once, clearly shown in his message (error messages generally being unhelpful:-). The configure is looking for gdImageCreateFromPng in the gd library and not finding it in his case. That function does exist in 1.8.3 so either the wrong library is insatlled, its picking up the wrong library or something else is going on. I emailed David asking for more information. Anyway, to repeat its not a JPEG problem and I haven't managed to duplicate the JPEG problem. I'll have a word with Peter about this (he's only next door) before posting to the group again about it. Alan From ableasby at hgmp.mrc.ac.uk Sun Jul 23 17:48:01 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Sun, 23 Jul 2000 22:48:01 +0100 (BST) Subject: compile problem Message-ID: <200007232148.WAA13378@bromine.hgmp.mrc.ac.uk> First, the solution. The prefix should have been /usr/local as "lib" is added automatically. We'll check the instructions and try to make this more clear. Secondly the GD/JPEG issue. The GNU configure checks for gdImageCreateFromPng by doing a sed search for the text directly on the library. If the library is not where specified (or in a standard directory) or doesn't contain this function then you'll get that error. With the supplied gd source you have to make a special effort to compile in jpeg support. If you did so and didn't have libjpeg* then, as that library is built statically, you'd get a compile error. If you forced the library to link dynamically you might not. Whether you'd get any unresolved runtime messages with EMBOSS would need further (rather pointless) tinkering. I suppose if you are having problems and want to eliminate a variable or two then compile the libraries statically (the gd default). Alan From diriano at ibun.unal.edu.co Sat Jul 29 09:35:22 2000 From: diriano at ibun.unal.edu.co (Diego Mauricio =?iso-8859-1?Q?Ria=F1o=20Pach=F3n?=) Date: Sat, 29 Jul 2000 08:35:22 -0500 Subject: Where is emboss.default? Message-ID: <3982DD99.199FCF9B@ibun.unal.edu.co> Hi everybody I had installed EMBOSS on a Linux 2.0.36, the installation is correct and running, but i can't find emboss.default. Somebody help me? I need to configure the access to the databases. Can i tell to the program thar search for databases online, on the web? Please answer to me private mail diriano at ibun.unal.edu.co Thanks in advances Diego Mauricio Ria?o Pach?n Biologist Bioinformatics Group Biotechnology Intitute National University of Colombia Santa Fe de Bogota Colombia South America From ggibbs at hgmp.mrc.ac.uk Tue Jul 4 10:39:56 2000 From: ggibbs at hgmp.mrc.ac.uk (Geoff Gibbs) Date: Tue, 4 Jul 2000 11:39:56 +0100 (BST) Subject: test Message-ID: <20000704103956.BD049FAF4@gold.hgmp.mrc.ac.uk> Alan, just to test that the emboss list works and that you are on it. Geoff From ableasby at hgmp.mrc.ac.uk Sat Jul 15 22:29:33 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Sat, 15 Jul 2000 23:29:33 +0100 (BST) Subject: EMBOSS has moved to HGMP Message-ID: <200007152229.XAA19252@bromine.hgmp.mrc.ac.uk> Dear EMBOSS folk, Yes, EMBOSS has indeed moved. Please note the new address for the web pages. It is: http://www.uk.embnet.org/Software/EMBOSS or if you prefer http://www.hgmp.mrc.ac.uk/Software/EMBOSS they are the same address. Similarly the ftp server becomes: ftp://ftp.uk.embnet.org/pub/EMBOSS or ftp://ftp.hgmp.mrc.ac.uk/pub/EMBOSS Why the move? It is because Peter Rice and Ian Longden have both just gone into the commercial sector. Peter has gone to Lion and Ian to Informatica. This left noone at Sanger with the experience to maintain EMBOSS therefore it finds a welcome home with the HGMP developers. I surely speak for all of us when I thank Peter and Ian for their work... although Peter will still be active with EMBOSS from the Lion point of view so this is neither an obituary or E.J. Thribb poem. Both still have their Sanger usernames intact for now. And so on to the changes. You will notice a different look and feel to the web pages. This is in preparation for the imminent announcement of Release 1.0.0. You will see this reflected in the filename of EMBOSS on the ftp server. It is EMBOSS-1.0.0.tar.gz N.B: As of this distribution there is an extra 'emboss' directory level at the top. This is to allow the --prefix configuration option to (optionally) install directories there. The instructions for use of the CVS server have also changed. Please read the new instructions on the web pages if you use this method. This server also has the extra directory mentioned above. Also note that there is no alias for cvs.hgmp.mrc.ac.uk at the moment i.e. cvs.uk.embnet.org will not work but the former will. The mail list addresses have changed accordingly. They are: emboss at uk.embnet.org emboss-dev at uk.embnet.org or emboss at hgmp.mrc.ac.uk emboss-dev at hgmp.mrc.ac.uk All the subscription addresses have been moved over. The majordomo server at our site works in the same way as on the Sanger site. N.B.: Until the Sanger site change their links to redirect to HGMP their site is still active. It is not being updated though. To get the latest updates you must use the new addresses. I am bound to have forgotten something as we've all had to work like demons to move things over and get to a stage where we can advertise release 1.0.0. I will post if anything important springs to mind. Finally, it is St Swithins Day so, if the new service works today it will probably work for the next 40. If not you can always email: emboss-bug at uk.embnet.org or emboss-bug at hgmp.mrc.ac.uk Cheers Alan HGMP From ableasby at hgmp.mrc.ac.uk Sun Jul 16 11:07:23 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Sun, 16 Jul 2000 12:07:23 +0100 (BST) Subject: Directory Levels Message-ID: <200007161107.MAA00672@bromine.hgmp.mrc.ac.uk> I made a slight error in the move announcement. There is no extra emboss directory level in the ftp distribution but there is in the CVS distribution. Alan From David.Lapointe at umassmed.edu Wed Jul 19 20:49:35 2000 From: David.Lapointe at umassmed.edu (Lapointe, David) Date: Wed, 19 Jul 2000 16:49:35 -0400 Subject: Compile problem Message-ID: For some reason, configure --with-pngdriver=/usr/local/lib ( where the z,libpng, and gd libs are) refuses to configure png checking for gdImageCreateFromPng in -lgd... no need to upgrade gd for png driver for plplot No png driver will be made due to librarys missing/old Well, it's not missing and it's not old ( gd 1.8.3 ). This is an IRIX 6.5 system. David Lapointe, Ph.D. Research Computing Manager 6-5141 "Great minds think a lot" From starksb at ebi.ac.uk Thu Jul 20 06:00:55 2000 From: starksb at ebi.ac.uk (David Starks-Browning) Date: Thu, 20 Jul 2000 07:00:55 +0100 Subject: Compile problem In-Reply-To: References: Message-ID: <1800-Thu20Jul2000070055+0100-starksb@ebi.ac.uk> On Wednesday 19 Jul 00, Lapointe, David writes: > For some reason, configure --with-pngdriver=/usr/local/lib ( where the > z,libpng, and gd > libs are) refuses to configure png > > checking for gdImageCreateFromPng in -lgd... no > need to upgrade gd for png driver for plplot > No png driver will be made due to librarys missing/old > > Well, it's not missing and it's not old ( gd 1.8.3 ). > > This is an IRIX 6.5 system. Just guessing here, because you don't provide enough details, but could it be that EMBOSS, and any of the existing z, png or gd libs in /usr/local/lib have different ABIs? If you don't know what I mean ('man abi' is a good start), let me know and I'll try to help you get it sorted. Cheers, David ------------------------------------------------------------------- David Starks-Browning | starksb at ebi.ac.uk EMBL Outstation -- | The European Bioinformatics Institute | Wellcome Trust Genome Campus | tel: +44 (1223) 494 616 Hinxton, Cambridge, CB10 1SD, UK | fax: +44 (1223) 494 468 ------------------------------------------------------------------- From ptribble at hgmp.mrc.ac.uk Thu Jul 20 08:14:42 2000 From: ptribble at hgmp.mrc.ac.uk (Peter C. Tribble) Date: Thu, 20 Jul 2000 09:14:42 +0100 (BST) Subject: Compile problem Message-ID: <20000720081442.1CC6F415DA@mercury.hgmp.mrc.ac.uk> David Lapointe said: >>>For some reason, configure --with-pngdriver=/usr/local/lib ( where the >>>z,libpng, and gd >>>libs are) refuses to configure png >>> >>>checking for gdImageCreateFromPng in -lgd... no >>>need to upgrade gd for png driver for plplot >>>No png driver will be made due to librarys missing/old >>> >>>Well, it's not missing and it's not old ( gd 1.8.3 ). It's too new, I suspect. gd 1.8.3 requires jpeg as well as png, and emboss doesn't know that yet. You should be able to look at config.log to work out what's gone wrong, but currently emboss won't work with gd 1.8.3. (I spotted this last week on OpenBSD, which didn't generate any link errors and cheerfully built emboss, but then none of the binaries would actually run because they couldn't find any of the jpeg stuff at runtime.) -Peter Tribble HGMP Computing Services http://www.hgmp.mrc.ac.uk/~ptribble/ From bauer at genprofile.com Thu Jul 20 08:24:44 2000 From: bauer at genprofile.com (David Bauer) Date: Thu, 20 Jul 2000 10:24:44 +0200 Subject: Compile problem References: <20000720081442.1CC6F415DA@mercury.hgmp.mrc.ac.uk> Message-ID: <3976B74C.6FE522FF@genprofile.com> "Peter C. Tribble" wrote: > out what's gone wrong, but currently emboss won't work with gd 1.8.3. Yup, that's new to me. I'm running emboss on FreeBSD with exactly this version of gd and it can create png output without problems. -- Dr. David Bauer GenProfile AG, Max-Delbrueck-Center, Erwin-Negelein-Haus Robert-Roessle-Str. 10, D-13125 Berlin, Germany bauer at genprofile.com, Tel:49-30-94892165, FAX:49-30-94892151 From ableasby at hgmp.mrc.ac.uk Thu Jul 20 08:56:08 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Thu, 20 Jul 2000 09:56:08 +0100 (BST) Subject: Compile problem Message-ID: <200007200856.JAA24845@bromine.hgmp.mrc.ac.uk> It is certainly nothing to do with JPEG. That is a problem I'm investigating (I can't get EMBOSS to fail with 1.8.3 at the moment either.) The problem David was happening was, for once, clearly shown in his message (error messages generally being unhelpful:-). The configure is looking for gdImageCreateFromPng in the gd library and not finding it in his case. That function does exist in 1.8.3 so either the wrong library is insatlled, its picking up the wrong library or something else is going on. I emailed David asking for more information. Anyway, to repeat its not a JPEG problem and I haven't managed to duplicate the JPEG problem. I'll have a word with Peter about this (he's only next door) before posting to the group again about it. Alan From ableasby at hgmp.mrc.ac.uk Sun Jul 23 21:48:01 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Sun, 23 Jul 2000 22:48:01 +0100 (BST) Subject: compile problem Message-ID: <200007232148.WAA13378@bromine.hgmp.mrc.ac.uk> First, the solution. The prefix should have been /usr/local as "lib" is added automatically. We'll check the instructions and try to make this more clear. Secondly the GD/JPEG issue. The GNU configure checks for gdImageCreateFromPng by doing a sed search for the text directly on the library. If the library is not where specified (or in a standard directory) or doesn't contain this function then you'll get that error. With the supplied gd source you have to make a special effort to compile in jpeg support. If you did so and didn't have libjpeg* then, as that library is built statically, you'd get a compile error. If you forced the library to link dynamically you might not. Whether you'd get any unresolved runtime messages with EMBOSS would need further (rather pointless) tinkering. I suppose if you are having problems and want to eliminate a variable or two then compile the libraries statically (the gd default). Alan From diriano at ibun.unal.edu.co Sat Jul 29 13:35:22 2000 From: diriano at ibun.unal.edu.co (Diego Mauricio =?iso-8859-1?Q?Ria=F1o=20Pach=F3n?=) Date: Sat, 29 Jul 2000 08:35:22 -0500 Subject: Where is emboss.default? Message-ID: <3982DD99.199FCF9B@ibun.unal.edu.co> Hi everybody I had installed EMBOSS on a Linux 2.0.36, the installation is correct and running, but i can't find emboss.default. Somebody help me? I need to configure the access to the databases. Can i tell to the program thar search for databases online, on the web? Please answer to me private mail diriano at ibun.unal.edu.co Thanks in advances Diego Mauricio Ria?o Pach?n Biologist Bioinformatics Group Biotechnology Intitute National University of Colombia Santa Fe de Bogota Colombia South America