[BioRuby] Ruby installation

[Russell Whitaker]

"Thanks for the security info. Luckily it does not affect my line of work."

So don't generalize your own practices as recommendations, perhaps? As
an aside, I'm surprised and skeptical of any claims that security
issues like buffer overflows have no relevance to their work, whatever
that might be.

"Maybe the described dependency hell in one of your other links is
more relevant to web-developers."

No, it's quite relevant to those of us using ruby without Rails as well.

Russell

On Tue, Apr 29, 2014 at 11:57 AM, Joachim Baran <joachim.baran at gmail.com> wrote:
> Hi!
>
>   Thanks for the security info. Luckily it does not affect my line of work.
>
>   Maybe the described dependency hell in one of your other links is more
> relevant to web-developers. I do not use Rails and have not encounters major
> problems in this regard.
>
> Kim
>
>
> On 29 April 2014 11:44, Russell Whitaker <russell.whitaker at gmail.com> wrote:
>>
>> Please tell me you're kidding: the default Mavericks /usr/bin/ruby is
>> "ruby 2.0.0p247 (2013-06-27 revision 41674)
>> [universal.x86_64-darwin13]", which contains a now well-known security
>> vulnerability:
>>
>> http://blog.rubygems.org/2013/09/09/CVE-2013-4287.html
>> http://www.scip.ch/en/?vuldb.11266
>>
>> Yes, the default "works out-of-the-box," but that's insufficient.
>> Every _professional_ ruby development shop uses some kind of ruby
>> version management, be it rvm, rbenv, chruby, or whatever.
>>
>> Friends don't let friends use system ruby:
>> http://robots.thoughtbot.com/psa-do-not-use-system-ruby
>>
>> "On Linux I usually just pick the latest Ruby interpreter and that works
>> then. Having said that, my Linux VMs usually do not last very long (purged
>> after the job is done), so I do not know how great the Linux eco-system
>> maintains versioning."
>>
>> Using the same ruby version management tools as above. Really.
>>
>> Russell
>>
>> On Tue, Apr 29, 2014 at 11:23 AM, Joachim Baran <joachim.baran at gmail.com>
>> wrote:
>> > Hey!
>> >
>> >   I wholeheartedly disagree. :)
>> >
>> >   I had to use rvm beforehand, because Ruby installations were a mess.
>> > However, with the newest Mac OS X I find that the up-to-date Ruby
>> > interpreter works really well -- including the gem system. MacPorts also
>> > installed some Ruby versions in its /opt hierarchy, but those are at the
>> > end of my $PATH and get ignored.
>> >
>> >   On Linux I usually just pick the latest Ruby interpreter and that
>> > works
>> > then. Having said that, my Linux VMs usually do not last very long
>> > (purged
>> > after the job is done), so I do not know how great the Linux eco-system
>> > maintains versioning.
>> >
>> >   So, from my perspective, Ruby is the easy choice that works
>> > out-of-the-box.
>> >
>> > Kim
>> >
>> >
>> > On 28 April 2014 22:14, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
>> >
>> >> Hi everyone,
>> >>
>> >> It used to be that Ruby was easy to install.
>> >>
>> >> But the last years I find people are having real trouble installing
>> >> Ruby and gems. I also run into odd annoyances, even if I can handle
>> >> rvm myself. I am running into this because I am teaching people to use
>> >> my gems :). I think it is too hard for a language that is supposed to
>> >> be easy.
>> >>
>> >> Anyone disagree?
>> >>
>> >> Can we develop a best practise protocol that works for our gems at
>> >> least on all Linux distributions? What would be the best way? And
>> >> maybe we can extend to OSX and Windows later.
>> >>
>> >> Homebrew would be nice, but it needs a good Ruby to bootstrap. RVM is
>> >> too tricky.
>> >>
>> >> Do we need to build from source, perhaps? Or start using GUIX?
>> >>
>> >> Any suggestions other then use my 'favorite' distribution are welcome.
>> >>
>> >> Pj.
>>
>> --
>> Russell Whitaker
>> http://twitter.com/OrthoNormalRuss
>> http://www.linkedin.com/pub/russell-whitaker/0/b86/329
>> _______________________________________________
>> BioRuby Project - http://www.bioruby.org/
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>
>



-- 
Russell Whitaker
http://twitter.com/OrthoNormalRuss
http://www.linkedin.com/pub/russell-whitaker/0/b86/329