Project

General

Profile

Bug #11165

gem install bio-samtools

Added by tbochan (Tad Bochan) over 5 years ago. Updated over 5 years ago.

Status:
Third Party's Issue
Priority:
Normal
Assignee:
-
Target version:
-
ruby -v:
ruby 2.3.0dev (2015-05-20 trunk 50560) [x86_64-linux]
[ruby-core:<unknown>]

Description

gem install bio-samtools works with ruby 2.1.2 but fails with 2.3.0

824 /home/tad : gem install bio-samtools
Building native extensions. This could take a while...
ERROR: Error installing bio-samtools:
ERROR: Failed to build gem native extension.

/home/tad/.rvm/rubies/ruby-head/bin/ruby mkrf_conf.rb

/home/tad/.rvm/rubies/ruby-head/bin/ruby -rubygems /home/tad/.rvm/gems/ruby-head@global/gems/rake-10.4.2/bin/rake RUBYARCHDIR=/home/tad/.rvm/gems/ruby-head/extensions/x86_64-linux/2.3.0/bio-samtools-2.3.2 RUBYLIBDIR=/home/tad/.rvm/gems/ruby-head/extensions/x86_64-linux/2.3.0/bio-samtools-2.3.2
:
:
:
samtools-0.1.19/bam.h~
cd samtools-0.1.19
patch < ../Makefile-bioruby.patch
patching file Makefile
patch < ../Makefile-suse.patch
patching file Makefile
Hunk #1 succeeded at 15 with fuzz 1 (offset 2 lines).
rake aborted!
NameError: uninitialized constant Config
/home/tad/.rvm/gems/ruby-head/gems/bio-samtools-2.3.2/ext/Rakefile:23:in block (2 levels) in <top (required)>'
/home/tad/.rvm/gems/ruby-head/gems/bio-samtools-2.3.2/ext/Rakefile:19:in
block in '
Tasks: TOP => default => compile
(See full trace by running task with --trace)

rake failed, exit code 1

Gem files will remain installed in /home/tad/.rvm/gems/ruby-head/gems/bio-samtools-2.3.2 for inspection.
Results logged to /home/tad/.rvm/gems/ruby-head/extensions/x86_64-linux/2.3.0/bio-samtools-2.3.2/gem_make.out

#1

Updated by tbochan (Tad Bochan) over 5 years ago

Also fails in the same way with : ruby 2.2.1p85 (2015-02-26 revision 49769) [x86_64-linux]

#2

Updated by Hanmac (Hans Mackowiak) over 5 years ago

that is not an error in ruby, but in the gem (so its a third-party problem)

please report it there:
https://github.com/helios/bioruby-samtools/issues

the solution would be to replace Config::CONFIG in mkrf_conf with RbConfig::CONFIG

#3

Updated by hsbt (Hiroshi SHIBATA) over 5 years ago

  • Status changed from Open to Third Party's Issue

Also available in: Atom PDF