OSX: With homebrew GeCode 4.x installed, gem doesn't work #22

danielsdeleo · 2014-04-16T22:58:28Z

NOTE this is copied from chef/dep-selector-libgecode#10

What happened

Install GeCode 4.x: brew install gecode
Install dep-selector-libgecode 1.0.0: gem install dep-selector-libgecode -v 1.0.0
Run ruby code that uses it (e.g. berks 3.0.0.rc1): berks

/usr/local/var/rbenv/versions/2.0.0-p451/lib/ruby/gems/2.0.0/gems/ffi-1.9.3/lib/ffi/library.rb:133:in `block in ffi_lib': Could not open library '/usr/local/var/rbenv/versions/2.
0.0-p451/lib/ruby/gems/2.0.0/gems/dep_selector-1.0.0/lib/dep_gecode.bundle': dlopen(/usr/local/var/rbenv/versions/2.0.0-p451/lib/ruby/gems/2.0.0/gems/dep_selector-1.0.0/lib/dep_g
ecode.bundle, 5): Symbol not found: __ZN6Gecode16ValBranchOptions3defE (LoadError)
  Referenced from: /usr/local/var/rbenv/versions/2.0.0-p451/lib/ruby/gems/2.0.0/gems/dep_selector-1.0.0/lib/dep_gecode.bundle
  Expected in: flat namespace

Workaround

uninstall 'dep-selector-libgecode': gem uninstall dep-selector-libgecode dep_selector
uninstall 'gecode': brew uninstall gecode
reinstall dep-selector-libgecode: gem install dep-selector-libgecode -v 1.0.0

Notes

I wonder if an RPATH isn't being set right or something.

The text was updated successfully, but these errors were encountered:

danielsdeleo · 2014-04-16T23:05:35Z

@docwhat This is caused by an issue in ruby. On this line: https://github.com/opscode/dep-selector/blob/master/ext/dep_gecode/extconf.rb#L31 we ask ruby to check if it can find the gecode library in dep-selector-libgecode. Ruby uses the value of RbConfig::MAKEFILE_CONFIG['RPATHFLAG'] to add path stuff for each path you add via find_library On my mac, RbConfig::MAKEFILE_CONFIG['RPATHFLAG'] == "" whereas on my linux box it's: " -Wl,-R%1$-s".

I'm at chefconf this week so I don't have a ton of free time, but I'd like to research whether there is a fix in ruby for this problem before trying to implement a workaround in dep-selector.

danielsdeleo · 2014-04-17T18:36:43Z

Also, this is pretty weird (results of otool -l $(gem which dep_gecode)):

/Users/ddeleo/.rbenv/versions/2.0.0-p247/lib/ruby/site_ruby/2.0.0/x86_64-darwin12.4.0/dep_gecode.bundle:
Load command 0
      cmd LC_SEGMENT_64
  cmdsize 712
  segname __TEXT
   vmaddr 0x0000000000000000
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            cmd LC_DYSYMTAB
        cmdsize 80
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  cmdsize 16
  version 10.9
      sdk 10.9
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      cmd LC_SOURCE_VERSION
  cmdsize 16
  version 0.0
Load command 9
          cmd LC_LOAD_DYLIB
      cmdsize 64
         name /usr/local/lib/libgecodesearch.32.dylib (offset 24)
   time stamp 2 Wed Dec 31 16:00:02 1969
      current version 32.0.0
compatibility version 32.0.0
Load command 10
          cmd LC_LOAD_DYLIB
      cmdsize 72
         name /usr/local/lib/libgecodeminimodel.32.dylib (offset 24)
   time stamp 2 Wed Dec 31 16:00:02 1969
      current version 32.0.0
compatibility version 32.0.0
Load command 11
          cmd LC_LOAD_DYLIB
      cmdsize 64
         name /usr/local/lib/libgecodeint.32.dylib (offset 24)
   time stamp 2 Wed Dec 31 16:00:02 1969
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compatibility version 32.0.0
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          cmd LC_LOAD_DYLIB
      cmdsize 64
         name /usr/local/lib/libgecodekernel.32.dylib (offset 24)
   time stamp 2 Wed Dec 31 16:00:02 1969
      current version 32.0.0
compatibility version 32.0.0
Load command 13
          cmd LC_LOAD_DYLIB
      cmdsize 72
         name /usr/local/lib/libgecodesupport.32.dylib (offset 24)
   time stamp 2 Wed Dec 31 16:00:02 1969
      current version 32.0.0
compatibility version 32.0.0
Load command 14
          cmd LC_LOAD_DYLIB
      cmdsize 56
         name /usr/lib/libSystem.B.dylib (offset 24)
   time stamp 2 Wed Dec 31 16:00:02 1969
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compatibility version 1.0.0
Load command 15
          cmd LC_LOAD_DYLIB
      cmdsize 56
         name /usr/lib/libobjc.A.dylib (offset 24)
   time stamp 2 Wed Dec 31 16:00:02 1969
      current version 228.0.0
compatibility version 1.0.0
Load command 16
          cmd LC_LOAD_DYLIB
      cmdsize 48
         name /usr/lib/libc++.1.dylib (offset 24)
   time stamp 2 Wed Dec 31 16:00:02 1969
      current version 120.0.0
compatibility version 1.0.0
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      cmd LC_FUNCTION_STARTS
  cmdsize 16
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 datasize 232
Load command 18
      cmd LC_DATA_IN_CODE
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 datasize 0
Load command 19
      cmd LC_DYLIB_CODE_SIGN_DRS
  cmdsize 16
  dataoff 128168
 datasize 288

Note this part:

Load command 13
          cmd LC_LOAD_DYLIB
      cmdsize 72
         name /usr/local/lib/libgecodesupport.32.dylib (offset 24)
   time stamp 2 Wed Dec 31 16:00:02 1969
      current version 32.0.0

That doesn't exist on my system.

danielsdeleo · 2014-04-17T21:18:39Z

@lamont-granquist any thoughts?

docwhat · 2014-04-17T22:14:17Z

I was thinking about it on the way home. It can't just be an RPATH problem or brew uninstall would fix it. And brew installing gecode afterwards would break it.

If your custom downloading/compiling gecode anyway, why not static link it?

docwhat · 2014-04-17T23:48:08Z

On my home laptop, I get:

$ otool -L /usr/local/var/rbenv/versions/2.0.0-p451/lib/ruby/gems/2.0.0/gems/dep_selector-1.0.2/lib/dep_gecode.bundle
/usr/local/var/rbenv/versions/2.0.0-p451/lib/ruby/gems/2.0.0/gems/dep_selector-1.0.2/lib/dep_gecode.bundle:
        /usr/local/var/rbenv/versions/2.0.0-p451/lib/ruby/gems/2.0.0/gems/dep-selector-libgecode-1.0.0/lib/dep-selector-libgecode/vendored-gecode/lib/libgecodesearch.32.dylib (compatibility version 32.0.0, current version 32.0.0)
        /usr/local/var/rbenv/versions/2.0.0-p451/lib/ruby/gems/2.0.0/gems/dep-selector-libgecode-1.0.0/lib/dep-selector-libgecode/vendored-gecode/lib/libgecodeminimodel.32.dylib (compatibility version 32.0.0, current version 32.0.0)
        /usr/local/var/rbenv/versions/2.0.0-p451/lib/ruby/gems/2.0.0/gems/dep-selector-libgecode-1.0.0/lib/dep-selector-libgecode/vendored-gecode/lib/libgecodeint.32.dylib (compatibility version 32.0.0, current version 32.0.0)
        /usr/local/var/rbenv/versions/2.0.0-p451/lib/ruby/gems/2.0.0/gems/dep-selector-libgecode-1.0.0/lib/dep-selector-libgecode/vendored-gecode/lib/libgecodekernel.32.dylib (compatibility version 32.0.0, current version 32.0.0)
        /usr/local/var/rbenv/versions/2.0.0-p451/lib/ruby/gems/2.0.0/gems/dep-selector-libgecode-1.0.0/lib/dep-selector-libgecode/vendored-gecode/lib/libgecodesupport.32.dylib (compatibility version 32.0.0, current version 32.0.0)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
        /usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)
        /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0)

danielsdeleo · 2014-04-19T00:59:32Z

Might be fixed by #26

nhuff · 2014-04-21T19:08:46Z

Just as another data point, on a Fedora 20 box with gecode 4 system package installed I couldn't get dep-solver gem to correctly link until I removed the gecode package and ruby -rrbconfig -e 'p RbConfig::MAKEFILE_CONFIG["RPATHFLAG"]' is " -Wl,-R%1$-s"

It looks lie the the gecode 4 package provides .so.36 libraries which dep-solver was preferentially linking to instead of the .so.32 included in the vendored version so setting LD_LIBRARY_PATH wasn't even an option. I had to remove the packages and then reinstall dep-solver.

hntd187 · 2014-04-23T23:42:38Z

I am also experiencing what appears to be this issue, but to no avail. When I try and run berks I get

/home/scarman/.rvm/gems/ruby-2.1.0/gems/ffi-1.9.3/lib/ffi/library.rb:133:in `block in ffi_lib': Could not open library '/home/scarman/.rvm/gems/ruby-2.1.0/bundler/gems/dep-selector-7a75df69ae48/lib/dep_gecode.so': libgecodesearch.so.32: cannot open shared object file: No such file or directory (LoadError)
    from /home/scarman/.rvm/gems/ruby-2.1.0/gems/ffi-1.9.3/lib/ffi/library.rb:100:in `map'
    from /home/scarman/.rvm/gems/ruby-2.1.0/gems/ffi-1.9.3/lib/ffi/library.rb:100:in `ffi_lib'
    from /home/scarman/.rvm/gems/ruby-2.1.0/bundler/gems/dep-selector-7a75df69ae48/lib/dep_selector/dep_gecode.rb:39:in `<module:Dep_gecode>'
    from /home/scarman/.rvm/gems/ruby-2.1.0/bundler/gems/dep-selector-7a75df69ae48/lib/dep_selector/dep_gecode.rb:21:in `<top (required)>'
    from /home/scarman/.rvm/gems/ruby-2.1.0/bundler/gems/dep-selector-7a75df69ae48/lib/dep_selector/gecode_wrapper.rb:21:in `require'
    from /home/scarman/.rvm/gems/ruby-2.1.0/bundler/gems/dep-selector-7a75df69ae48/lib/dep_selector/gecode_wrapper.rb:21:in `<top (required)>'
    from /home/scarman/.rvm/gems/ruby-2.1.0/bundler/gems/dep-selector-7a75df69ae48/lib/dep_selector/dependency_graph.rb:21:in `require'
    from /home/scarman/.rvm/gems/ruby-2.1.0/bundler/gems/dep-selector-7a75df69ae48/lib/dep_selector/dependency_graph.rb:21:in `<top (required)>'
    from /home/scarman/.rvm/gems/ruby-2.1.0/bundler/gems/dep-selector-7a75df69ae48/lib/dep_selector/selector.rb:21:in `require'
    from /home/scarman/.rvm/gems/ruby-2.1.0/bundler/gems/dep-selector-7a75df69ae48/lib/dep_selector/selector.rb:21:in `<top (required)>'
    from /home/scarman/.rvm/gems/ruby-2.1.0/bundler/gems/dep-selector-7a75df69ae48/lib/dep_selector.rb:22:in `require'
    from /home/scarman/.rvm/gems/ruby-2.1.0/bundler/gems/dep-selector-7a75df69ae48/lib/dep_selector.rb:22:in `<top (required)>'
    from /home/scarman/.rvm/gems/ruby-2.1.0/gems/solve-1.2.0/lib/solve/solver.rb:1:in `require'
    from /home/scarman/.rvm/gems/ruby-2.1.0/gems/solve-1.2.0/lib/solve/solver.rb:1:in `<top (required)>'
    from /home/scarman/.rvm/gems/ruby-2.1.0/gems/solve-1.2.0/lib/solve.rb:10:in `require_relative'
    from /home/scarman/.rvm/gems/ruby-2.1.0/gems/solve-1.2.0/lib/solve.rb:10:in `<module:Solve>'
    from /home/scarman/.rvm/gems/ruby-2.1.0/gems/solve-1.2.0/lib/solve.rb:3:in `<top (required)>'
    from /home/scarman/.rvm/gems/ruby-2.1.0/bundler/gems/berkshelf-c1063cb4fa84/lib/berkshelf.rb:8:in `require'
    from /home/scarman/.rvm/gems/ruby-2.1.0/bundler/gems/berkshelf-c1063cb4fa84/lib/berkshelf.rb:8:in `<top (required)>'
    from /home/scarman/.rvm/gems/ruby-2.1.0/bundler/gems/berkshelf-c1063cb4fa84/lib/berkshelf/cli.rb:1:in `require'
    from /home/scarman/.rvm/gems/ruby-2.1.0/bundler/gems/berkshelf-c1063cb4fa84/lib/berkshelf/cli.rb:1:in `<top (required)>'
    from /home/scarman/.rvm/gems/ruby-2.1.0/bundler/gems/berkshelf-c1063cb4fa84/bin/berks:3:in `require'
    from /home/scarman/.rvm/gems/ruby-2.1.0/bundler/gems/berkshelf-c1063cb4fa84/bin/berks:3:in `<top (required)>'
    from /home/scarman/.rvm/gems/ruby-2.1.0/bin/berks:23:in `load'
    from /home/scarman/.rvm/gems/ruby-2.1.0/bin/berks:23:in `<main>'
    from /home/scarman/.rvm/gems/ruby-2.1.0/bin/ruby_executable_hooks:15:in `eval'
    from /home/scarman/.rvm/gems/ruby-2.1.0/bin/ruby_executable_hooks:15:in `<main>'

Uninstall of the gecode doesn't do anything. When I reinstall the gem I get this

gem install dep-selector-libgecode -v 1.0.0
Fetching: dep-selector-libgecode-1.0.0.gem (100%)
Building native extensions.  This could take a while...
Successfully installed dep-selector-libgecode-1.0.0
Parsing documentation for dep-selector-libgecode-1.0.0
unable to convert "\xE9" from ASCII-8BIT to UTF-8 for ext/libgecode3/vendor/gecode-3.7.3/Makefile, skipping
unable to convert "\xEB" from ASCII-8BIT to UTF-8 for ext/libgecode3/vendor/gecode-3.7.3/changelog.in, skipping
unable to convert "\x8E" from ASCII-8BIT to UTF-8 for ext/libgecode3/vendor/gecode-3.7.3/contribs/qecode/QCOPPlus.cc, skipping
unable to convert "\xFC" from ASCII-8BIT to UTF-8 for ext/libgecode3/vendor/gecode-3.7.3/examples/bin-packing.cpp, skipping
unable to convert "\xEA" from ASCII-8BIT to UTF-8 for ext/libgecode3/vendor/gecode-3.7.3/examples/black-hole.cpp, skipping
unable to convert "\xD6" from ASCII-8BIT to UTF-8 for ext/libgecode3/vendor/gecode-3.7.3/examples/dominating-queens.cpp, skipping
unable to convert "\xEF" from ASCII-8BIT to UTF-8 for ext/libgecode3/vendor/gecode-3.7.3/gecode.m4, skipping
unable to convert "\xED" from ASCII-8BIT to UTF-8 for ext/libgecode3/vendor/gecode-3.7.3/gecode/int.hh, skipping
unable to convert "\xED" from ASCII-8BIT to UTF-8 for ext/libgecode3/vendor/gecode-3.7.3/gecode/int/cumulative.hh, skipping
unable to convert "\xE9" from ASCII-8BIT to UTF-8 for ext/libgecode3/vendor/gecode-3.7.3/gecode/int/distinct.hh, skipping
unable to convert "\xF3" from ASCII-8BIT to UTF-8 for ext/libgecode3/vendor/gecode-3.7.3/gecode/int/gcc.hh, skipping
unable to convert "\xE4" from ASCII-8BIT to UTF-8 for ext/libgecode3/vendor/gecode-3.7.3/gecode/int/sorted.hh, skipping
unable to convert "\xED" from ASCII-8BIT to UTF-8 for ext/libgecode3/vendor/gecode-3.7.3/gecode/int/unary.hh, skipping
unable to convert "\xED" from ASCII-8BIT to UTF-8 for lib/dep-selector-libgecode/vendored-gecode/include/gecode/int.hh, skipping
unable to convert "\xED" from ASCII-8BIT to UTF-8 for lib/dep-selector-libgecode/vendored-gecode/include/gecode/int/cumulative.hh, skipping
unable to convert "\xE9" from ASCII-8BIT to UTF-8 for lib/dep-selector-libgecode/vendored-gecode/include/gecode/int/distinct.hh, skipping
unable to convert "\xF3" from ASCII-8BIT to UTF-8 for lib/dep-selector-libgecode/vendored-gecode/include/gecode/int/gcc.hh, skipping
unable to convert "\xE4" from ASCII-8BIT to UTF-8 for lib/dep-selector-libgecode/vendored-gecode/include/gecode/int/sorted.hh, skipping
unable to convert "\xED" from ASCII-8BIT to UTF-8 for lib/dep-selector-libgecode/vendored-gecode/include/gecode/int/unary.hh, skipping
Installing ri documentation for dep-selector-libgecode-1.0.0
Done installing documentation for dep-selector-libgecode after 10 seconds
1 gem installed

Hopefully this is relevant.

danielsdeleo · 2014-04-23T23:46:11Z

All the stuff after Parsing documentation for dep-selector-libgecode-1.0.0 is just noise, rdoc is trying to parse binary files and gecode source as if it were ruby to generate documentation. I've been looking for the right rdoc options to suppress that, but haven't gotten it working yet.

danielsdeleo · 2014-04-23T23:53:16Z

@hntd187 I think your issue is different than this one. If you had this issue you'd be seeing Symbol not found: __ZN6Gecode16ValBranchOptions3defE or something like that. Can you create a new ticket, and include the output of bundle show dep-selector-libgecode and readelf -d home/scarman/.rvm/gems/ruby-2.1.0/bundler/gems/dep-selector-7a75df69ae48/lib/dep_gecode.so

hntd187 · 2014-04-24T00:22:23Z

@danielsdeleo Well you are correct, but also when I run something like kitchen list for chef test kitchen I get the symbol error that you are describing here. I'm just trying to add extra information to what you are talking about.

cscetbon · 2014-05-05T14:05:48Z

Hi,

any news about it ?

petere · 2014-05-05T15:07:46Z

The workaround listed at the top worked for me.

cscetbon · 2014-05-05T15:22:17Z

Right ! sorry, I didn't see the workaround part but only the issue and the following posts ..

Thanks

Cyril SCETBON

On 05 May 2014, at 17:07, Peter Eisentraut [email protected] wrote:

The workaround listed at the top worked for me.

—
Reply to this email directly or view it on GitHub.

lamont-granquist · 2014-05-29T17:01:20Z

you can lazy load the library with DL.dlopen instead of linking it at link-time:

https://github.com/lamont-granquist/ffi-yajl/blob/master/lib/ffi_yajl/ext.rb#L16

if you go down that route it has the advantage that when the dep-selector-libgecode gem is updated then it'll update the 'link' from dep-selector as well, rather than having dep-selector fixed to a version of libgecode at its install time.

there's issues with windows begin stupid and needing a shim to be able to do lazy linking.

latest ruby yanks DL.dlopen out of the standard library, however, and we have to use fiddle instead, and i haven't ported to that yet.

Ellison001 · 2015-06-11T06:34:12Z

I got the similar error here. and the workaround listed at the top doesn't work for me.
!!!!! The berkshelf' gem is missing and must be installed or cannot be properly activated. Rungem install berkshelfor add the following to your Gemfile if you are using Bundler:gem 'berkshelf'`.

------Exception-------
Class: Kitchen::UserError
Message: Could not load or activate Berkshelf (Could not open library '/Users/ezhang/.chefdk/gem/ruby/2.1.0/gems/dep_selector-1.0.3/lib/dep_gecode.bundle': dlopen(/Users/ezhang/.chefdk/gem/ruby/2.1.0/gems/dep_selector-1.0.3/lib/dep_gecode.bundle, 5): Library not loaded: /usr/local/lib/libgecodesearch.36.dylib
Referenced from: /Users/ezhang/.chefdk/gem/ruby/2.1.0/gems/dep_selector-1.0.3/lib/dep_gecode.bundle
Reason: image not found)

erinnovations · 2015-08-25T12:00:55Z

same problem here :(

dbafast · 2015-11-20T20:51:46Z

OSX
Same issue .
Is this fixed?

------Exception-------
Class: Kitchen::UserError
Message: Could not load or activate Berkshelf (Could not open library '/Library/Ruby/Gems/2.0.0/gems/dep_selector-1.0.3/lib/dep_gecode.bundle': dlopen(/Library/Ruby/Gems/2.0.0/gems/dep_selector-1.0.3/lib/dep_gecode.bundle, 5): Library not loaded: /private/var/folders/q6/_4hvkps50mvdwgq1kq35x_000000gr/T/bundler20151023-6196-1t2v8ysdep-selector-libgecode-1.0.2/gems/dep-selector-libgecode-1.0.2/lib/dep-selector-libgecode/vendored-gecode/lib/libgecodesearch.32.dylib

danielsdeleo mentioned this issue May 5, 2014

Could not open library dep_gecode.bundle #19

Closed

shawnzhu mentioned this issue Oct 23, 2014

Library not loaded. Reason: image not found berkshelf/berkshelf#1234

Closed

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OSX: With homebrew GeCode 4.x installed, gem doesn't work #22

OSX: With homebrew GeCode 4.x installed, gem doesn't work #22

danielsdeleo commented Apr 16, 2014

danielsdeleo commented Apr 16, 2014

danielsdeleo commented Apr 17, 2014

danielsdeleo commented Apr 17, 2014

docwhat commented Apr 17, 2014

docwhat commented Apr 17, 2014

danielsdeleo commented Apr 19, 2014

nhuff commented Apr 21, 2014

hntd187 commented Apr 23, 2014

danielsdeleo commented Apr 23, 2014

danielsdeleo commented Apr 23, 2014

hntd187 commented Apr 24, 2014

cscetbon commented May 5, 2014

petere commented May 5, 2014

cscetbon commented May 5, 2014

lamont-granquist commented May 29, 2014

Ellison001 commented Jun 11, 2015

erinnovations commented Aug 25, 2015

dbafast commented Nov 20, 2015

OSX: With homebrew GeCode 4.x installed, gem doesn't work #22

OSX: With homebrew GeCode 4.x installed, gem doesn't work #22

Comments

danielsdeleo commented Apr 16, 2014

What happened

Workaround

Notes

danielsdeleo commented Apr 16, 2014

danielsdeleo commented Apr 17, 2014

danielsdeleo commented Apr 17, 2014

docwhat commented Apr 17, 2014

docwhat commented Apr 17, 2014

danielsdeleo commented Apr 19, 2014

nhuff commented Apr 21, 2014

hntd187 commented Apr 23, 2014

danielsdeleo commented Apr 23, 2014

danielsdeleo commented Apr 23, 2014

hntd187 commented Apr 24, 2014

cscetbon commented May 5, 2014

petere commented May 5, 2014

cscetbon commented May 5, 2014

Thanks

lamont-granquist commented May 29, 2014

Ellison001 commented Jun 11, 2015

erinnovations commented Aug 25, 2015

dbafast commented Nov 20, 2015