From schnober at elda.org Fri Sep 24 06:27:19 2010 From: schnober at elda.org (Carsten Schnober) Date: Fri, 24 Sep 2010 12:27:19 +0200 Subject: [BioCatalogue-hackers] Gem problems Message-ID: <4C9C7D07.6010500@elda.org> Hi list, I am setting up a local Biocatalogue server on an Ubuntu 10.04 system. Following the instructions on (1), I installed the Ubuntu Ruby package, but RubyGems 1.3.7 from rubygems.org and subsequently the gems listed in the installation instructions. However, when starting the server later on, it apparently does not properly find the gems which leads to a Mongrel crash. The debugging output leads me to the suspicion that the gems are searched in /usr/local/lib/site_ruby/1.8/; RubyGems, however, installs them in /usr/lib/ruby/gems. Setting the environment variable GEM_HOME to the latter path does not make a difference. I suppose this is because there is no file rubygems.rb in /usr/lib/ruby/gems, so Ruby apparently falls back to the one available in /usr/local/lib/site_ruby/1.8. I know that this is rather a RubyGems/Ubuntu than an actual BioCatalogue issue, but I suppose the instructions regarding the RubyGems installation have been given for a good reason. Maybe someone can point me towards a proper solution before I am messing up my system's packaging system. I am attaching the debugging output. Thanks a lot, Carsten (1) http://www.biocatalogue.org/wiki/doku.php?id=development:installation#ubuntu_10.04 -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: biocatalogue.debug URL: From jits at cs.man.ac.uk Mon Sep 27 09:47:22 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 27 Sep 2010 14:47:22 +0100 Subject: [BioCatalogue-hackers] Gem problems In-Reply-To: <4C9C7D07.6010500@elda.org> References: <4C9C7D07.6010500@elda.org> Message-ID: <4CA0A06A.7030701@cs.man.ac.uk> Hi Carsten, Thanks for providing the detailed information on the problem you're experiencing. We will try and replicate this locally and get back to you. (I've used Ubuntu extensively for the development of the BioCatalogue and never come across this before, so hopefully it's an isolated thing). Thanks for your patience. Cheers, Jits Carsten Schnober wrote: > Hi list, > I am setting up a local Biocatalogue server on an Ubuntu 10.04 system. > Following the instructions on (1), I installed the Ubuntu Ruby package, > but RubyGems 1.3.7 from rubygems.org and subsequently the gems listed in > the installation instructions. > However, when starting the server later on, it apparently does not > properly find the gems which leads to a Mongrel crash. The debugging > output leads me to the suspicion that the gems are searched in > /usr/local/lib/site_ruby/1.8/; RubyGems, however, installs them in > /usr/lib/ruby/gems. > Setting the environment variable GEM_HOME to the latter path does not > make a difference. I suppose this is because there is no file > rubygems.rb in /usr/lib/ruby/gems, so Ruby apparently falls back to the > one available in /usr/local/lib/site_ruby/1.8. > > I know that this is rather a RubyGems/Ubuntu than an actual BioCatalogue > issue, but I suppose the instructions regarding the RubyGems > installation have been given for a good reason. Maybe someone can point > me towards a proper solution before I am messing up my system's > packaging system. > I am attaching the debugging output. > Thanks a lot, > Carsten > > > (1) > http://www.biocatalogue.org/wiki/doku.php?id=development:installation#ubuntu_10.04 > > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-hackers mailing list > BioCatalogue-hackers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-hackers From jits at cs.man.ac.uk Mon Sep 27 10:21:18 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 27 Sep 2010 15:21:18 +0100 Subject: [BioCatalogue-hackers] Gem problems In-Reply-To: <4C9C7D07.6010500@elda.org> References: <4C9C7D07.6010500@elda.org> Message-ID: <4CA0A85E.6050309@cs.man.ac.uk> Hi again Carsten, It occurs to me that we missed out the step where you have to install the Ruby on Rails gems (!). Could you try running this: sudo gem install rails -v 2.3.2 ... and then testing the server again, please? Let us know how it goes. Cheers, Jits Carsten Schnober wrote: > Hi list, > I am setting up a local Biocatalogue server on an Ubuntu 10.04 system. > Following the instructions on (1), I installed the Ubuntu Ruby package, > but RubyGems 1.3.7 from rubygems.org and subsequently the gems listed in > the installation instructions. > However, when starting the server later on, it apparently does not > properly find the gems which leads to a Mongrel crash. The debugging > output leads me to the suspicion that the gems are searched in > /usr/local/lib/site_ruby/1.8/; RubyGems, however, installs them in > /usr/lib/ruby/gems. > Setting the environment variable GEM_HOME to the latter path does not > make a difference. I suppose this is because there is no file > rubygems.rb in /usr/lib/ruby/gems, so Ruby apparently falls back to the > one available in /usr/local/lib/site_ruby/1.8. > > I know that this is rather a RubyGems/Ubuntu than an actual BioCatalogue > issue, but I suppose the instructions regarding the RubyGems > installation have been given for a good reason. Maybe someone can point > me towards a proper solution before I am messing up my system's > packaging system. > I am attaching the debugging output. > Thanks a lot, > Carsten > > > (1) > http://www.biocatalogue.org/wiki/doku.php?id=development:installation#ubuntu_10.04 > > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-hackers mailing list > BioCatalogue-hackers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-hackers From jits at cs.man.ac.uk Mon Sep 27 10:24:59 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 27 Sep 2010 15:24:59 +0100 Subject: [BioCatalogue-hackers] Gem problems In-Reply-To: <4CA0A85E.6050309@cs.man.ac.uk> References: <4C9C7D07.6010500@elda.org> <4CA0A85E.6050309@cs.man.ac.uk> Message-ID: <4CA0A93B.1060501@cs.man.ac.uk> Carsten, My apologies, please ignore my suggestion below; the required Rails libraries are embedded "within" the BioCatalogue source code so you wouldn't need to carry out the step below. I will continue investigating your error. Jits Jiten Bhagat wrote: > Hi again Carsten, > > It occurs to me that we missed out the step where you have to install > the Ruby on Rails gems (!). > > Could you try running this: > > sudo gem install rails -v 2.3.2 > > ... and then testing the server again, please? > > Let us know how it goes. > > Cheers, > Jits > > > > Carsten Schnober wrote: > >> Hi list, >> I am setting up a local Biocatalogue server on an Ubuntu 10.04 system. >> Following the instructions on (1), I installed the Ubuntu Ruby package, >> but RubyGems 1.3.7 from rubygems.org and subsequently the gems listed in >> the installation instructions. >> However, when starting the server later on, it apparently does not >> properly find the gems which leads to a Mongrel crash. The debugging >> output leads me to the suspicion that the gems are searched in >> /usr/local/lib/site_ruby/1.8/; RubyGems, however, installs them in >> /usr/lib/ruby/gems. >> Setting the environment variable GEM_HOME to the latter path does not >> make a difference. I suppose this is because there is no file >> rubygems.rb in /usr/lib/ruby/gems, so Ruby apparently falls back to the >> one available in /usr/local/lib/site_ruby/1.8. >> >> I know that this is rather a RubyGems/Ubuntu than an actual BioCatalogue >> issue, but I suppose the instructions regarding the RubyGems >> installation have been given for a good reason. Maybe someone can point >> me towards a proper solution before I am messing up my system's >> packaging system. >> I am attaching the debugging output. >> Thanks a lot, >> Carsten >> >> >> (1) >> http://www.biocatalogue.org/wiki/doku.php?id=development:installation#ubuntu_10.04 >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> BioCatalogue-hackers mailing list >> BioCatalogue-hackers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-hackers >> > > > From schnober at elda.org Tue Sep 28 03:43:33 2010 From: schnober at elda.org (Carsten Schnober) Date: Tue, 28 Sep 2010 09:43:33 +0200 Subject: [BioCatalogue-hackers] Gem problems In-Reply-To: <4CA0A93B.1060501@cs.man.ac.uk> References: <4C9C7D07.6010500@elda.org> <4CA0A85E.6050309@cs.man.ac.uk> <4CA0A93B.1060501@cs.man.ac.uk> Message-ID: <4CA19CA5.7010103@elda.org> Hi Jits, thank you very much for investigating this issue. Something that has come into my mind: it might have to do with my Ruby version. On Ubuntu, do you usually use the Ubuntu packaged Ruby version or do you compile and install it yourself? Thanks, Carsten From schnober at elda.org Tue Sep 28 05:18:22 2010 From: schnober at elda.org (Carsten Schnober) Date: Tue, 28 Sep 2010 11:18:22 +0200 Subject: [BioCatalogue-hackers] Gem problems In-Reply-To: <4CA0A93B.1060501@cs.man.ac.uk> References: <4C9C7D07.6010500@elda.org> <4CA0A85E.6050309@cs.man.ac.uk> <4CA0A93B.1060501@cs.man.ac.uk> Message-ID: <4CA1B2DE.7030503@elda.org> Hi, another probably related problem has occurred to me that I have not described clearly in my initial error diagnosis: I cannot even start the solr server. When doing 'rake solr:start', I get an error message 'undefined method `closed?' for nil:NilClass'. I am attaching the full error message log from 'rake --trace solr:start' Thanks again, Carsten -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: solr.err URL: From jits at cs.man.ac.uk Tue Sep 28 05:22:12 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 28 Sep 2010 10:22:12 +0100 Subject: [BioCatalogue-hackers] Gem problems In-Reply-To: <4CA19CA5.7010103@elda.org> References: <4C9C7D07.6010500@elda.org> <4CA0A85E.6050309@cs.man.ac.uk> <4CA0A93B.1060501@cs.man.ac.uk> <4CA19CA5.7010103@elda.org> Message-ID: <4CA1B3C4.1030400@cs.man.ac.uk> Hi Carsten, Carsten Schnober wrote: > Hi Jits, > thank you very much for investigating this issue. Something that has > come into my mind: it might have to do with my Ruby version. On Ubuntu, > do you usually use the Ubuntu packaged Ruby version or do you compile > and install it yourself? > I tend to use the Ubuntu packaged Ruby version, and with Ruby Version Manager (RVM) [1] installed with various versions of Ruby (so I can work with and test out the projects on different Rubies). If you have the Ubuntu packaged Ruby it *should* work. Still haven't been able to reproduce this but will spend more time on this today and tomorrow. Cheers, Jits [1] http://rvm.beginrescueend.com/ > Thanks, > Carsten > > From jits at cs.man.ac.uk Tue Sep 28 05:25:36 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 28 Sep 2010 10:25:36 +0100 Subject: [BioCatalogue-hackers] Gem problems In-Reply-To: <4CA1B2DE.7030503@elda.org> References: <4C9C7D07.6010500@elda.org> <4CA0A85E.6050309@cs.man.ac.uk> <4CA0A93B.1060501@cs.man.ac.uk> <4CA1B2DE.7030503@elda.org> Message-ID: <4CA1B490.9080007@cs.man.ac.uk> Hi Carsten, This seems to point to some major issues with the installation of Ruby that you have. This line (from your original email)... (eval):3: [BUG] gc_sweep(): unknown data type 0x0(0x7f7bced35d00) ... doesn't seem like a "normal" error. Did you by any chance upgrade your Ubuntu installation from an older version (to 10.04)? Let me set up a fresh virtual machine with Ubuntu 10.04 and try setting up by following the instructions. Cheers, Jits Carsten Schnober wrote: > Hi, > another probably related problem has occurred to me that I have not > described clearly in my initial error diagnosis: > I cannot even start the solr server. When doing 'rake solr:start', I get > an error message 'undefined method `closed?' for nil:NilClass'. > I am attaching the full error message log from 'rake --trace solr:start' > Thanks again, > Carsten > From schnober at elda.org Tue Sep 28 05:51:56 2010 From: schnober at elda.org (Carsten Schnober) Date: Tue, 28 Sep 2010 11:51:56 +0200 Subject: [BioCatalogue-hackers] Gem problems In-Reply-To: <4CA1B490.9080007@cs.man.ac.uk> References: <4C9C7D07.6010500@elda.org> <4CA0A85E.6050309@cs.man.ac.uk> <4CA0A93B.1060501@cs.man.ac.uk> <4CA1B2DE.7030503@elda.org> <4CA1B490.9080007@cs.man.ac.uk> Message-ID: <4CA1BABC.60304@elda.org> On 28/09/2010 11:25, Jiten Bhagat wrote: Hi, > This seems to point to some major issues with the installation of Ruby > that you have. > > This line (from your original email)... > > (eval):3: [BUG] gc_sweep(): unknown data type 0x0(0x7f7bced35d00) > > ... doesn't seem like a "normal" error. > > Did you by any chance upgrade your Ubuntu installation from an older > version (to 10.04)? Just a quick answer in order to reduce the potential errors: No, I did not upgrade the system, only Ubuntu 10.04 was installed. Neither did I use or install Ruby on the system before I started dealing with Biocatalogue. Kind regards, Carsten From jits at cs.man.ac.uk Tue Sep 28 05:56:36 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 28 Sep 2010 10:56:36 +0100 Subject: [BioCatalogue-hackers] Gem problems In-Reply-To: <4CA1BABC.60304@elda.org> References: <4C9C7D07.6010500@elda.org> <4CA0A85E.6050309@cs.man.ac.uk> <4CA0A93B.1060501@cs.man.ac.uk> <4CA1B2DE.7030503@elda.org> <4CA1B490.9080007@cs.man.ac.uk> <4CA1BABC.60304@elda.org> Message-ID: <4CA1BBD4.3050406@cs.man.ac.uk> Carsten Schnober wrote: > On 28/09/2010 11:25, Jiten Bhagat wrote: > > Hi, > > >> This seems to point to some major issues with the installation of Ruby >> that you have. >> >> This line (from your original email)... >> >> (eval):3: [BUG] gc_sweep(): unknown data type 0x0(0x7f7bced35d00) >> >> ... doesn't seem like a "normal" error. >> >> Did you by any chance upgrade your Ubuntu installation from an older >> version (to 10.04)? >> > > Just a quick answer in order to reduce the potential errors: No, I did > not upgrade the system, only Ubuntu 10.04 was installed. > Neither did I use or install Ruby on the system before I started dealing > with Biocatalogue. > Kind regards, > OK, thanks Carsten, that's useful to know. I'm hoping it's just a simple error in the instructions that has caused this. Will get back to you on this :-) Cheers, Jits > Carsten > > From jits at cs.man.ac.uk Tue Sep 28 08:54:07 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 28 Sep 2010 13:54:07 +0100 Subject: [BioCatalogue-hackers] Gem problems In-Reply-To: <4CA1BBD4.3050406@cs.man.ac.uk> References: <4C9C7D07.6010500@elda.org> <4CA0A85E.6050309@cs.man.ac.uk> <4CA0A93B.1060501@cs.man.ac.uk> <4CA1B2DE.7030503@elda.org> <4CA1B490.9080007@cs.man.ac.uk> <4CA1BABC.60304@elda.org> <4CA1BBD4.3050406@cs.man.ac.uk> Message-ID: <4CA1E56F.7090707@cs.man.ac.uk> Hi again Carsten, Unfortunately, it turns out that the Ruby version in Ubuntu is very outdated and has some bugs that have since been fixed :-( This is the cause of the issue you are getting with starting up Solr (ref: http://redmine.ruby-lang.org/issues/show/2708). I have added a hack into our codebase to tackle this so if you do an svn update and then try starting up solr it should now work. As for your original errors, I'm unable to reproduce this in a fresh virtual machine. Would you be able to send me the output of running: gem env ... please? Also, are you in a position to uninstall and reinstall all the Ruby, RubyGems and gems stuff? Cheers, Jits Jiten Bhagat wrote: > Carsten Schnober wrote: > >> On 28/09/2010 11:25, Jiten Bhagat wrote: >> >> Hi, >> >> >> >>> This seems to point to some major issues with the installation of Ruby >>> that you have. >>> >>> This line (from your original email)... >>> >>> (eval):3: [BUG] gc_sweep(): unknown data type 0x0(0x7f7bced35d00) >>> >>> ... doesn't seem like a "normal" error. >>> >>> Did you by any chance upgrade your Ubuntu installation from an older >>> version (to 10.04)? >>> >>> >> Just a quick answer in order to reduce the potential errors: No, I did >> not upgrade the system, only Ubuntu 10.04 was installed. >> Neither did I use or install Ruby on the system before I started dealing >> with Biocatalogue. >> Kind regards, >> >> > > OK, thanks Carsten, that's useful to know. > > I'm hoping it's just a simple error in the instructions that has caused > this. Will get back to you on this :-) > > Cheers, > Jits > > >> Carsten >> >> >> > > _______________________________________________ > BioCatalogue-hackers mailing list > BioCatalogue-hackers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-hackers > From schnober at elda.org Tue Sep 28 09:31:38 2010 From: schnober at elda.org (Carsten Schnober) Date: Tue, 28 Sep 2010 15:31:38 +0200 Subject: [BioCatalogue-hackers] Gem problems In-Reply-To: <4CA1E56F.7090707@cs.man.ac.uk> References: <4C9C7D07.6010500@elda.org> <4CA0A85E.6050309@cs.man.ac.uk> <4CA0A93B.1060501@cs.man.ac.uk> <4CA1B2DE.7030503@elda.org> <4CA1B490.9080007@cs.man.ac.uk> <4CA1BABC.60304@elda.org> <4CA1BBD4.3050406@cs.man.ac.uk> <4CA1E56F.7090707@cs.man.ac.uk> Message-ID: <4CA1EE3A.9090607@elda.org> On 28/09/2010 14:54, Jiten Bhagat wrote: > Unfortunately, it turns out that the Ruby version in Ubuntu is very > outdated and has some bugs that have since been fixed :-( This is the > cause of the issue you are getting with starting up Solr (ref: > http://redmine.ruby-lang.org/issues/show/2708). I have added a hack into > our codebase to tackle this so if you do an svn update and then try > starting up solr it should now work. Thanks, the solr server is now running for me. Although it gave a warning 'Running a 32-bit JVM is not supported on this platform.' Seems to do no harm though. > As for your original errors, I'm unable to reproduce this in a fresh > virtual machine. Would you be able to send me the output of running: > > gem env > > ... please? Sure, I am attaching the output. > Also, are you in a position to uninstall and reinstall all the Ruby, > RubyGems and gems stuff? I am and I have just re-installed all the gems. However, this is a machine that runs a couple of other services, so I will not be able to re-install the OS etc. But Ruby is not in use otherwise, so no problem with that. Any more hints? Do you think taking the effort of compiling my own Ruby installation might help? Thanks, Carsten -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: gemenv.txt URL: From jits at cs.man.ac.uk Tue Sep 28 09:44:25 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 28 Sep 2010 14:44:25 +0100 Subject: [BioCatalogue-hackers] Gem problems In-Reply-To: <4CA1EE3A.9090607@elda.org> References: <4C9C7D07.6010500@elda.org> <4CA0A85E.6050309@cs.man.ac.uk> <4CA0A93B.1060501@cs.man.ac.uk> <4CA1B2DE.7030503@elda.org> <4CA1B490.9080007@cs.man.ac.uk> <4CA1BABC.60304@elda.org> <4CA1BBD4.3050406@cs.man.ac.uk> <4CA1E56F.7090707@cs.man.ac.uk> <4CA1EE3A.9090607@elda.org> Message-ID: <4CA1F139.7050902@cs.man.ac.uk> Carsten Schnober wrote: > On 28/09/2010 14:54, Jiten Bhagat wrote: > > >> Unfortunately, it turns out that the Ruby version in Ubuntu is very >> outdated and has some bugs that have since been fixed :-( This is the >> cause of the issue you are getting with starting up Solr (ref: >> http://redmine.ruby-lang.org/issues/show/2708). I have added a hack into >> our codebase to tackle this so if you do an svn update and then try >> starting up solr it should now work. >> > > Thanks, the solr server is now running for me. Although it gave a > warning 'Running a 32-bit JVM is not supported on this platform.' > Seems to do no harm though. > Ahh yes, the dev one is set to run in 32-bit. You can modify it to run on 64-bit by editing config/solr.yml. (Let me know if you need help with this). > >> As for your original errors, I'm unable to reproduce this in a fresh >> virtual machine. Would you be able to send me the output of running: >> >> gem env >> >> ... please? >> > > Sure, I am attaching the output. > This looks fine to me. > >> Also, are you in a position to uninstall and reinstall all the Ruby, >> RubyGems and gems stuff? >> > > I am and I have just re-installed all the gems. However, this is a > machine that runs a couple of other services, so I will not be able to > re-install the OS etc. But Ruby is not in use otherwise, so no problem > with that. Any more hints? Do you think taking the effort of compiling > my own Ruby installation might help? > I understand. We'll try and do things in a very isolated fashion so it doesn't affect anything else. My recommendation at this stage would be to uninstall Ruby and RubyGems and reinstall these using the instructions provided on the BioCat set up wiki page. If this doesn't work I can provide some instructions on how to quickly set up Ruby Version Manager (this can be installed only in your user profile and can be run in such a way that it doesn't affect anything else on your machine). We can then use this to run the BioCatalogue application on Ruby 1.8.6 (which we can guarantee it works on). Cheers, Jits > Thanks, > Carsten >