Re: [EMBOSS] HELP! fdnapars fails with undefined symbol error - ajSeqdbInit
Now when I run the application I get this error in fdnapars: "Error: Unable to read sequence '/var/lib/emboss-explorer/output/672342/.sequence' Died: fdnapars terminated: Bad value for ' -sequence' with -auto defined" I looked in that directory and all that was in there was a .sequence file that looked just fine (it was my input file)any ideas what went wrong? Running fdnapars from the command line also results in an error reading the sequence file (it's one I use for testing, worked fine previously) Wolfgang Dr. Wolfgang Rumpf Product Specialist, Rescentris Inc. Adjunct Faculty, Dept. of Biotechnology, UMUC wolfgang.ru...@rescentris.com wolfgang.ru...@gmail.com Mobile - (614) 638-6797 Skype - wolfgang.rumpf On Mar 11, 2011, at 10:54 AM, Charles Plessy wrote: > Le Thu, Mar 10, 2011 at 09:26:44PM -0500, Wolfgang Rumpf a écrit : >> Also tried and failed - apparently there were dependencies that >> couldn't be resolved. > > I have prepared unofficial backports of EMBOSS 6.3.1 and EMBASSY-PHYLIP 3.69 > > https://launchpad.net/~plessy/+archive/plessy/+sourcepub/1547062/+listing-archive-extra > https://launchpad.net/~plessy/+archive/plessy/+sourcepub/1547739/+listing-archive-extra > > (the second one is scheduled to be built in 2 hours, so I can not guarantee > that it > will be available) > > Can you try them ? > > Have a nice day, > > -- > Charles Plessy > Debian Med packaging team, > http://www.debian.org/devel/debian-med > Tsurumi, Kanagawa, Japan ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] HELP! fdnapars fails with undefined symbol error - ajSeqdbInit
Le Thu, Mar 10, 2011 at 09:26:44PM -0500, Wolfgang Rumpf a écrit : > Also tried and failed - apparently there were dependencies that > couldn't be resolved. I have prepared unofficial backports of EMBOSS 6.3.1 and EMBASSY-PHYLIP 3.69 https://launchpad.net/~plessy/+archive/plessy/+sourcepub/1547062/+listing-archive-extra https://launchpad.net/~plessy/+archive/plessy/+sourcepub/1547739/+listing-archive-extra (the second one is scheduled to be built in 2 hours, so I can not guarantee that it will be available) Can you try them ? Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] HELP! fdnapars fails with undefined symbol error - ajSeqdbInit
Also tried and failed - apparently there were dependencies that couldn't be resolved. On 03/09/2011 08:37 PM, Charles Plessy wrote: Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a écrit : RE: undefined symbol: ajSeqdbInit While not an expert at all, on Emboss code, this type of error is typically due to (Emboss) binaries Not Yet being compiled with the newer linux-header resources. Pending that compilation by the Emboss maintenance team, if you run the compile from Emboss source code on your own Ubuntu 10.10 system, all will likely be OK. Dear Wolfgang, you can also give a try to the emboss and embassy-phylip from 11.04 Ubuntu distribution. If you can install them on 10.10, they should work well, and they are up to date. http://packages.ubuntu.com/natty/emboss http://packages.ubuntu.com/natty/embassy-phylip Have a nice day, ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] HELP! fdnapars fails with undefined symbol error - ajSeqdbInit
Everything I have tried has failed. I have uninstalled and reinstalled the entire EMBOSS/EMBASSY suite. I have booted from the previous kernel. Recompilation is a bit beyond me, I fear - what are the chances that this will just be fixed when 11.04 rolls out? Has anyone else had this problem? What's perplexing is that this has happened on both of my Ubuntu systems; there's nothing that was caused by me "tinkering" - this happened after the update to 10.10. Why didn't this get caught - am I the only person using Phylip in Emboss Explorer? On 03/10/2011 06:48 PM, Marvin Stodolsky wrote: There is a: http://packages.ubuntu.com/maverick/libnucleus6 $ sudo apt-get update $ sudo apt-get libnucleus6 should do all necessary. MarvS On Thu, Mar 10, 2011 at 1:27 PM, Henrikki Almusa wrote: On 2011-03-10 17:26, Wolfgang Rumpf wrote: So as I understand it my options are: 1. Boot with an older kernel - probably the latest one from 10.4, if it works with 10.10; 2. Recompile EMBOSS myself; 3. Download and install the 11.04 (unreleased) Emboss/Embassy installs; 4. Wait for 11.04 to come out Of all of these the "simplest" (other than just waiting) would probably be to try to boot with an older kernel - I don't want to bring the rest of the EMBOSS system down for an extended time period, perhaps very extended if the compilation/install doesn't go as planned. Sound about right? The error message complains about missing library file libnucleus.so.6 which was probably removed in update as there was no dependency on it (within the package lists). So here's a way to fix it: - go to packages.ubuntu.com and search for a package with file called libnucleus.so.6 - get result which tells you that it is in package libnucleus6 - install that named package with your favourite tool (for example apt-get) Wolfgang Dr. Wolfgang Rumpf Product Specialist, Rescentris Inc. wolfgang.ru...@rescentris.com Mobile - (614) 638-6797 Skype - wolfgang.rumpf On Mar 9, 2011, at 8:37 PM, Charles Plessy wrote: Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a écrit : RE: undefined symbol: ajSeqdbInit While not an expert at all, on Emboss code, this type of error is typically due to (Emboss) binaries Not Yet being compiled with the newer linux-header resources. Pending that compilation by the Emboss maintenance team, if you run the compile from Emboss source code on your own Ubuntu 10.10 system, all will likely be OK. Dear Wolfgang, you can also give a try to the emboss and embassy-phylip from 11.04 Ubuntu distribution. If you can install them on 10.10, they should work well, and they are up to date. http://packages.ubuntu.com/natty/emboss http://packages.ubuntu.com/natty/embassy-phylip Have a nice day, -- Charles Plessy Debian Med packaging team http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss -- Henrikki Almusa ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] HELP! fdnapars fails with undefined symbol error - ajSeqdbInit
There is a: http://packages.ubuntu.com/maverick/libnucleus6 $ sudo apt-get update $ sudo apt-get libnucleus6 should do all necessary. MarvS On Thu, Mar 10, 2011 at 1:27 PM, Henrikki Almusa wrote: > On 2011-03-10 17:26, Wolfgang Rumpf wrote: >> >> So as I understand it my options are: >> >> 1. Boot with an older kernel - probably the latest one from 10.4, if it >> works with 10.10; >> 2. Recompile EMBOSS myself; >> 3. Download and install the 11.04 (unreleased) Emboss/Embassy installs; >> 4. Wait for 11.04 to come out >> >> Of all of these the "simplest" (other than just waiting) would probably be >> to try to boot with an older kernel - I don't want to bring the rest of the >> EMBOSS system down for an extended time period, perhaps very extended if the >> compilation/install doesn't go as planned. >> >> Sound about right? > > The error message complains about missing library file libnucleus.so.6 which > was probably removed in update as there was no dependency on it (within the > package lists). So here's a way to fix it: > - go to packages.ubuntu.com and search for a package with file called > libnucleus.so.6 > - get result which tells you that it is in package libnucleus6 > - install that named package with your favourite tool (for example apt-get) > > >> Wolfgang >> >> Dr. Wolfgang Rumpf >> Product Specialist, Rescentris Inc. >> >> wolfgang.ru...@rescentris.com >> >> Mobile - (614) 638-6797 >> Skype - wolfgang.rumpf >> >> >> >> >> On Mar 9, 2011, at 8:37 PM, Charles Plessy wrote: >> >>> Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a écrit : RE: undefined symbol: ajSeqdbInit While not an expert at all, on Emboss code, this type of error is typically due to (Emboss) binaries Not Yet being compiled with the newer linux-header resources. Pending that compilation by the Emboss maintenance team, if you run the compile from Emboss source code on your own Ubuntu 10.10 system, all will likely be OK. >>> >>> Dear Wolfgang, >>> >>> you can also give a try to the emboss and embassy-phylip from 11.04 >>> Ubuntu >>> distribution. If you can install them on 10.10, they should work well, >>> and >>> they are up to date. >>> >>> http://packages.ubuntu.com/natty/emboss >>> http://packages.ubuntu.com/natty/embassy-phylip >>> >>> Have a nice day, >>> >>> -- >>> Charles Plessy >>> Debian Med packaging team >>> http://www.debian.org/devel/debian-med >>> Tsurumi, Kanagawa, Japan >>> ___ >>> EMBOSS mailing list >>> EMBOSS@lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/emboss >> >> >> ___ >> EMBOSS mailing list >> EMBOSS@lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss >> > > > -- > Henrikki Almusa > > ___ > EMBOSS mailing list > EMBOSS@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] HELP! fdnapars fails with undefined symbol error - ajSeqdbInit
On 2011-03-10 17:26, Wolfgang Rumpf wrote: So as I understand it my options are: 1. Boot with an older kernel - probably the latest one from 10.4, if it works with 10.10; 2. Recompile EMBOSS myself; 3. Download and install the 11.04 (unreleased) Emboss/Embassy installs; 4. Wait for 11.04 to come out Of all of these the "simplest" (other than just waiting) would probably be to try to boot with an older kernel - I don't want to bring the rest of the EMBOSS system down for an extended time period, perhaps very extended if the compilation/install doesn't go as planned. Sound about right? The error message complains about missing library file libnucleus.so.6 which was probably removed in update as there was no dependency on it (within the package lists). So here's a way to fix it: - go to packages.ubuntu.com and search for a package with file called libnucleus.so.6 - get result which tells you that it is in package libnucleus6 - install that named package with your favourite tool (for example apt-get) Wolfgang Dr. Wolfgang Rumpf Product Specialist, Rescentris Inc. wolfgang.ru...@rescentris.com Mobile - (614) 638-6797 Skype - wolfgang.rumpf On Mar 9, 2011, at 8:37 PM, Charles Plessy wrote: Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a écrit : RE: undefined symbol: ajSeqdbInit While not an expert at all, on Emboss code, this type of error is typically due to (Emboss) binaries Not Yet being compiled with the newer linux-header resources. Pending that compilation by the Emboss maintenance team, if you run the compile from Emboss source code on your own Ubuntu 10.10 system, all will likely be OK. Dear Wolfgang, you can also give a try to the emboss and embassy-phylip from 11.04 Ubuntu distribution. If you can install them on 10.10, they should work well, and they are up to date. http://packages.ubuntu.com/natty/emboss http://packages.ubuntu.com/natty/embassy-phylip Have a nice day, -- Charles Plessy Debian Med packaging team http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss -- Henrikki Almusa ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] HELP! fdnapars fails with undefined symbol error - ajSeqdbInit
Wolfgang > 1. Boot with an older kernel - probably the latest one from 10.4, if it > works with 10.10; really is expected to be trouble free. Linux strives to maintain backward compatibility. In the course of aiding modem users, I have and boot with numerous older kernels on my Systems. Your worst case scenario is that a bootup with an older kernel will fail. Then you will have to reboot with the current one. Merely having an older kernel installed will IN NO WAY interfere with usage of more recent kernels. Marvin On Thu, Mar 10, 2011 at 10:26 AM, Wolfgang Rumpf wrote: > So as I understand it my options are: > > 1. Boot with an older kernel - probably the latest one from 10.4, if it > works with 10.10; > 2. Recompile EMBOSS myself; > 3. Download and install the 11.04 (unreleased) Emboss/Embassy installs; > 4. Wait for 11.04 to come out > > Of all of these the "simplest" (other than just waiting) would probably be to > try to boot with an older kernel - I don't want to bring the rest of the > EMBOSS system down for an extended time period, perhaps very extended if the > compilation/install doesn't go as planned. > > Sound about right? > > Wolfgang > > Dr. Wolfgang Rumpf > Product Specialist, Rescentris Inc. > > wolfgang.ru...@rescentris.com > > Mobile - (614) 638-6797 > Skype - wolfgang.rumpf > > > > > On Mar 9, 2011, at 8:37 PM, Charles Plessy wrote: > >> Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a écrit : >>> >>> RE: undefined symbol: ajSeqdbInit >>> While not an expert at all, on Emboss code, >>> this type of error is typically due to (Emboss) binaries Not Yet >>> being compiled with the newer linux-header resources. Pending that >>> compilation by the Emboss maintenance team, if you run the compile >>> from Emboss source code on your own Ubuntu 10.10 system, all will >>> likely be OK. >> >> Dear Wolfgang, >> >> you can also give a try to the emboss and embassy-phylip from 11.04 Ubuntu >> distribution. If you can install them on 10.10, they should work well, and >> they are up to date. >> >> http://packages.ubuntu.com/natty/emboss >> http://packages.ubuntu.com/natty/embassy-phylip >> >> Have a nice day, >> >> -- >> Charles Plessy >> Debian Med packaging team >> http://www.debian.org/devel/debian-med >> Tsurumi, Kanagawa, Japan >> ___ >> EMBOSS mailing list >> EMBOSS@lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss > > > ___ > EMBOSS mailing list > EMBOSS@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] HELP! fdnapars fails with undefined symbol error - ajSeqdbInit
So as I understand it my options are: 1. Boot with an older kernel - probably the latest one from 10.4, if it works with 10.10; 2. Recompile EMBOSS myself; 3. Download and install the 11.04 (unreleased) Emboss/Embassy installs; 4. Wait for 11.04 to come out Of all of these the "simplest" (other than just waiting) would probably be to try to boot with an older kernel - I don't want to bring the rest of the EMBOSS system down for an extended time period, perhaps very extended if the compilation/install doesn't go as planned. Sound about right? Wolfgang Dr. Wolfgang Rumpf Product Specialist, Rescentris Inc. wolfgang.ru...@rescentris.com Mobile - (614) 638-6797 Skype - wolfgang.rumpf On Mar 9, 2011, at 8:37 PM, Charles Plessy wrote: > Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a écrit : >> >> RE: undefined symbol: ajSeqdbInit >> While not an expert at all, on Emboss code, >> this type of error is typically due to (Emboss) binaries Not Yet >> being compiled with the newer linux-header resources. Pending that >> compilation by the Emboss maintenance team, if you run the compile >> from Emboss source code on your own Ubuntu 10.10 system, all will >> likely be OK. > > Dear Wolfgang, > > you can also give a try to the emboss and embassy-phylip from 11.04 Ubuntu > distribution. If you can install them on 10.10, they should work well, and > they are up to date. > > http://packages.ubuntu.com/natty/emboss > http://packages.ubuntu.com/natty/embassy-phylip > > Have a nice day, > > -- > Charles Plessy > Debian Med packaging team > http://www.debian.org/devel/debian-med > Tsurumi, Kanagawa, Japan > ___ > EMBOSS mailing list > EMBOSS@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] HELP! fdnapars fails with undefined symbol error - ajSeqdbInit
Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a écrit : > > RE: undefined symbol: ajSeqdbInit > While not an expert at all, on Emboss code, > this type of error is typically due to (Emboss) binaries Not Yet > being compiled with the newer linux-header resources. Pending that > compilation by the Emboss maintenance team, if you run the compile > from Emboss source code on your own Ubuntu 10.10 system, all will > likely be OK. Dear Wolfgang, you can also give a try to the emboss and embassy-phylip from 11.04 Ubuntu distribution. If you can install them on 10.10, they should work well, and they are up to date. http://packages.ubuntu.com/natty/emboss http://packages.ubuntu.com/natty/embassy-phylip Have a nice day, -- Charles Plessy Debian Med packaging team http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] HELP! fdnapars fails with undefined symbol error - ajSeqdbInit
Wolfgang RE: undefined symbol: ajSeqdbInit While not an expert at all, on Emboss code, this type of error is typically due to (Emboss) binaries Not Yet being compiled with the newer linux-header resources. Pending that compilation by the Emboss maintenance team, if you run the compile from Emboss source code on your own Ubuntu 10.10 system, all will likely be OK. Check if linux-headers are installed on your System with: $ sudo apt-get update $ sudo apt-get install linux-headers-$(uname -r) You could also just reinstall and boot under the last kernel supporting Emboss. Typically linux is backward compatible to prior kernels, for a considerable period. Just search out the prior linux-image package at: http://packages.ubuntu.com MarvS scanModem maintainer On Wed, Mar 9, 2011 at 3:00 PM, Wolfgang Rumpf wrote: > I have an Emboss installation I'm using for teaching purposes. It was > working just fine until a few days ago, when I updated my OS to Ubuntu 10.10 > (from 10.4). Now I'm getting this error, specifically when I run fdnapars. > I'm worried that more might be broken, and I can't find anything useful via > google when I search for the error. Can anyone shed some light on what's > going on here? > > fdnapars: symbol lookup error: /usr/lib/libnucleus.so.6: undefined > symbol: ajSeqdbInit > > > > Cheers, > > Wolfgang > > -- > Wolfgang Rumpf, Ph.D. > Product Specialist, Rescentris Inc > Adjunct Faculty, UMUC Dept. of Biotechnology > -- > ___ > EMBOSS mailing list > EMBOSS@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
