# Bioruby-Name error: uninitialized constant **URL:** \ **Category:** Ruby\ **Created:** [February 22, 2008, 11:58am UTC](https://www.ruby-forum.com/t/bioruby-name-error-uninitialized-constant/129884 "2008-02-22T11:58:33Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![calvin76](https://www.ruby-forum.com/letter_avatar_proxy/v4/letter/c/9de053/32.png) [@calvin76](https://www.ruby-forum.com/u/calvin76)\ **Post date:** [February 22, 2008, 11:58am UTC](https://www.ruby-forum.com/t/bioruby-name-error-uninitialized-constant/129884/1 "2008-02-22T11:58:33Z")
I’m very new to both programming in general and to programming in Ruby. I have tried to write a programme in BioRuby: require ‘bio’ fasta = open(’…/sequence.fasta’) fasta\_string = fasta.read a = Bio::Alignment::MultiFastaFormat.new(fasta\_string).alignment a.each\_site do|bases\_at\_site| puts bases\_at\_site.join(’’) When I run the programme in irb, I get the following output: irb(main):001:0\> require ‘bio’ =\> true irb(main):002:0\> irb(main):003:0\* fasta = open(’…/sequence.fasta’) =\> #\ irb(main):004:0\> fasta\_string = fasta.read =\> "\>ref|NT\_039674.7|Mm18\_39714\_37:58262030-58293988 Mus musculus chromosome 18 genomic contig, strain C57BL/6J\r\nTTTCTATTTCAGCAGAAAAAAAAAAAGACGACTAGTCTTTGGGTT #I cut out the rest of the file since it’s very long. irb(main):005:0\> irb(main):006:0\* a = Bio::Alignment::MultiFastaFormat.new(fasta\_string).alignment NameError: uninitialized constant Bio::Alignment::MultiFastaFormat from (irb):6 irb(main):007:0\> irb(main):008:0\* a.each\_site do|bases\_at\_site| irb(main):009:1\* puts bases\_at\_site.join(’’) The solution is probably very simple, but I have played around with the code for half a day now and can’t get any further. I realise that the problem is with how I have used Bio::Alignment, but not sure where I have gone wrong. ---
**Author:** ![calvin76](https://www.ruby-forum.com/letter_avatar_proxy/v4/letter/c/9de053/32.png) [@calvin76](https://www.ruby-forum.com/u/calvin76)\ **Post date:** [February 22, 2008, 1:00pm UTC](https://www.ruby-forum.com/t/bioruby-name-error-uninitialized-constant/129884/2 "2008-02-22T13:00:25Z")
On Fri, Feb 22, 2008 at 11:58 AM, Carl O. [removed\_email\_address@domain.invalid](mailto:removed_email_address@domain.invalid) wrote: > I’m very new to both programming in general and to programming in Ruby. \> \> The solution is probably very simple, but I have played around with the \> code for half a day now and can't get any further. I realise that the \> problem is with how I have used Bio::Alignment, but not sure where I \> have gone wrong. \> I don’t know anything about BioRuby, but I took nonetheless a look at the gem. Did you take a look at the tutorial? You can view it with the gem server. Just type > gem server > in you console and you can access the RDocs of all your installed gems > at [http://localhost:8808/](http://localhost:8808/). Maybe you can find your solution there. Regards, Thomas ---
**Author:** ![calvin76](https://www.ruby-forum.com/letter_avatar_proxy/v4/letter/c/9de053/32.png) [@calvin76](https://www.ruby-forum.com/u/calvin76)\ **Post date:** [February 22, 2008, 4:53pm UTC](https://www.ruby-forum.com/t/bioruby-name-error-uninitialized-constant/129884/3 "2008-02-22T16:53:34Z")
I get the same problem if I install with “gem install bioruby” (which installs bioruby 0.6.4). If I do “gem install bio”, which installs bioruby 1.2.1, I don’t have the problem. (I didn’t actually try loading anything, but Bio::Alignment::MultiFastaFormat produces an uninitialized constant error in the first case, and refers to a real class in the second.) ---
**Author:** ![calvin76](https://www.ruby-forum.com/letter_avatar_proxy/v4/letter/c/9de053/32.png) [@calvin76](https://www.ruby-forum.com/u/calvin76)\ **Post date:** [February 25, 2008, 3:27pm UTC](https://www.ruby-forum.com/t/bioruby-name-error-uninitialized-constant/129884/4 "2008-02-25T15:27:51Z")
Christopher D. wrote: > I get the same problem if I install with “gem install bioruby” (which > installs bioruby 0.6.4). If I do “gem install bio”, which installs > bioruby 1.2.1, I don’t have the problem. > > (I didn’t actually try loading anything, but > Bio::Alignment::MultiFastaFormat produces an uninitialized constant > error in the first case, and refers to a real class in the second.) I managed to get rid of the error message by just adding the line: require ‘rubygems’ as a first line in the code. I’m not sure exactly why this works, but the advice was given by one of my supervisors. I don’t have administrator’s access to my computer so I cannot install any updates without going via the IT department, something that usually takes a couple of days. ---
**Author:** ![calvin76](https://www.ruby-forum.com/letter_avatar_proxy/v4/letter/c/9de053/32.png) [@calvin76](https://www.ruby-forum.com/u/calvin76)\ **Post date:** [February 25, 2008, 11:55pm UTC](https://www.ruby-forum.com/t/bioruby-name-error-uninitialized-constant/129884/5 "2008-02-25T23:55:16Z")
Carl O. wrote: > I managed to get rid of the error message by just adding the line: > > require ‘rubygems’ > > as a first line in the code. I’m not sure exactly why this works, but > the advice was given by one of my supervisors. I don’t have > administrator’s access to my computer so I cannot install any updates > without going via the IT department, something that usually takes a > couple of days. You must require ‘rubygems’ for any libraries that are installed as gems. -Justin ---
**Author:** ![calvin76](https://www.ruby-forum.com/letter_avatar_proxy/v4/letter/c/9de053/32.png) [@calvin76](https://www.ruby-forum.com/u/calvin76)\ **Post date:** [February 26, 2008, 12:21am UTC](https://www.ruby-forum.com/t/bioruby-name-error-uninitialized-constant/129884/6 "2008-02-26T00:21:45Z")
On Mon, Feb 25, 2008 at 11:53 PM, Justin C. [removed\_email\_address@domain.invalid](mailto:removed_email_address@domain.invalid) wrote: > You must require ‘rubygems’ for any libraries that are installed as gems. If you don’t set the enviroment variable RUBYOPT to ‘-rubygems’