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SuperNEMO-DBD / homebrew-cadfael

Instructions on using/installing the SuperNEMO Software are now at: https://github.com/SuperNEMO-DBD/brew
MIT License
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flsimulate can't find Bayeux library #14

Closed cherylepatrick closed 7 years ago

cherylepatrick commented 7 years ago

I've installed Falaise/Bayeux 3.0 (on MacOSX Sierra) and I think it was successful. However flsimulate can't find the Bayeux library: dyld: Library not loaded: @rpath/libBayeux.3.dylib Referenced from: /Users/cpatrick/CadfaelBrew/bin/flsimulate Reason: image not found Abort trap: 6

That library exists but is in /Users/cpatrick/CadfaelBrew/lib rather than bin. Do I need to set up some environment variable or something to tell it to look there? I cleared out my LD_LIBRARY_PATH and DYLD_LIBRARY_PATH (which pointed to the root5 directories for reasons I no longer recall), but it made no difference. Thanks in advance for suggestions!

drbenmorgan commented 7 years ago

Could you try running 

$ brew log -n5

and

$ brew config

and post the output here please? This looks like an error that should have been resolved by a commit in the main brew repository.

cherylepatrick commented 7 years ago

eduroam-int-dhcp-97-252-40:~ cpatrick$ brew log -n5 Warning: The git repository is a shallow clone therefore the filtering may be incorrect. Use git fetch --unshallow to get the full repository. commit 59c9ddbc1d9b9dfdeb0514768e0efd0112c63b25 Author: Shaun Jackman sjackman@gmail.com Date: Fri Mar 31 12:07:19 2017 -0700

Use --env=super by default for Linuxbrew

commit ff96869a878aa723a40fff553a6c51158baa982f Author: Shaun Jackman sjackman@gmail.com Date: Fri Mar 31 12:06:20 2017 -0700

Revert "Add env :super for Linuxbrew (#270)"

This reverts commit 09b6b09247ba0b21f81116e812d109818b634c6c.

commit 609d5e7524ba334a5b469825a068710d98d6a37b Author: Shaun Jackman sjackman@gmail.com Date: Sat Apr 8 09:14:04 2017 -0700

linkage: Add to the host white list for Linuxbrew

Add libcrypt.so.1 libnsl.so.1 libutil.so.1

commit bb231cb3d0fa1b341a6f48210400106b7aff503a Author: Shaun Jackman sjackman@gmail.com Date: Thu Apr 6 22:20:57 2017 -0700

Use unzip not homebrew/dupes/unzip for Linuxbrew (#330)

commit 3f4726e2374ba938aa3973d8ca5ff052056df876 Author: Shaun Jackman sjackman@gmail.com Date: Thu Apr 6 15:41:03 2017 -0700

linkage: Expand the host whitelist for Linuxbrew

eduroam-int-dhcp-97-252-40:~ cpatrick$ brew config HOMEBREW_VERSION: 1.1.11 ORIGIN: https://github.com/SuperNEMO-DBD/brew.git HEAD: 59c9ddbc1d9b9dfdeb0514768e0efd0112c63b25 Last commit: 4 weeks ago Core tap ORIGIN: https://github.com/Homebrew/homebrew-core Core tap HEAD: 12f5aebe20d2a2916b43da2d3c43c6a665f680f3 Core tap last commit: 22 hours ago HOMEBREW_PREFIX: /Users/cpatrick/CadfaelBrew HOMEBREW_REPOSITORY: /Users/cpatrick/CadfaelBrew HOMEBREW_CELLAR: /Users/cpatrick/CadfaelBrew/Cellar HOMEBREW_BOTTLE_DOMAIN: https://homebrew.bintray.com CPU: quad-core 64-bit broadwell Homebrew Ruby: 2.0.0-p648 Clang: 8.1 build 802 Git: 2.11.0 => /Applications/Xcode.app/Contents/Developer/usr/bin/git Perl: /usr/bin/perl Python: /Users/cpatrick/CadfaelBrew/bin/python => /Users/cpatrick/CadfaelBrew/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/bin/python2.7 Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby Java: N/A macOS: 10.12.4-x86_64 Xcode: 8.3.2 CLT: 8.3.2.0.1.1492020469 X11: 2.7.11 => /opt/X11

cherylepatrick commented 7 years ago

Also I ran brew update: eduroam-int-dhcp-97-252-40:~ cpatrick$ brew update Updated 1 tap (homebrew/core). ==> Updated Formulae arangodb gnome-recipes macvim svtplay-dl yaz at-spi2-atk immortal make tcpreplay at-spi2-core influxdb opencore-amr tippecanoe convox kobalt pwntools vault fabio libsoup serveit vice

drbenmorgan commented 7 years ago

O.k., just to double check, could you run

$ git -C $(brew --prefix) fetch --unshallow

and run the brew log -n5 command again please? Also, what's the output of 

$ git -C $(brew --prefix) remote -v

What the config output is showing is that brew appears to be on a tag version, and you have commits that aren't in SuperNEMO's brew.

cherylepatrick commented 7 years ago

eduroam-int-dhcp-97-252-40:~ cpatrick$ git -C $(brew --prefix) fetch --unshallow remote: Counting objects: 32, done. remote: Compressing objects: 100% (10/10), done. remote: Total 32 (delta 23), reused 31 (delta 22), pack-reused 0 Unpacking objects: 100% (32/32), done. eduroam-int-dhcp-97-252-40:~ cpatrick$ brew log -n5 commit 59c9ddbc1d9b9dfdeb0514768e0efd0112c63b25 Author: Shaun Jackman sjackman@gmail.com Date: Fri Mar 31 12:07:19 2017 -0700

Use --env=super by default for Linuxbrew

commit ff96869a878aa723a40fff553a6c51158baa982f Author: Shaun Jackman sjackman@gmail.com Date: Fri Mar 31 12:06:20 2017 -0700

Revert "Add env :super for Linuxbrew (#270)"

This reverts commit 09b6b09247ba0b21f81116e812d109818b634c6c.

commit 609d5e7524ba334a5b469825a068710d98d6a37b Author: Shaun Jackman sjackman@gmail.com Date: Sat Apr 8 09:14:04 2017 -0700

linkage: Add to the host white list for Linuxbrew

Add libcrypt.so.1 libnsl.so.1 libutil.so.1

commit bb231cb3d0fa1b341a6f48210400106b7aff503a Author: Shaun Jackman sjackman@gmail.com Date: Thu Apr 6 22:20:57 2017 -0700

Use unzip not homebrew/dupes/unzip for Linuxbrew (#330)

commit 3f4726e2374ba938aa3973d8ca5ff052056df876 Author: Shaun Jackman sjackman@gmail.com Date: Thu Apr 6 15:41:03 2017 -0700

linkage: Expand the host whitelist for Linuxbrew

eduroam-int-dhcp-97-252-40:~ cpatrick$ git -C $(brew --prefix) remote -v Linuxbrew https://github.com/Linuxbrew/brew.git (fetch) Linuxbrew https://github.com/Linuxbrew/brew.git (push) origin https://github.com/SuperNEMO-DBD/brew.git (fetch) origin https://github.com/SuperNEMO-DBD/brew.git (push)

I wonder if I did something odd with this in the past and checked out a weird version, and now it is coming back to bite me?

drbenmorgan commented 7 years ago

I think that's the case, I'm not sure why the "Linuxbrew" remote would be there (it's just possible there's a bug, but I think testing would have picked that up). What I'd suggest is:

  1. Do git -C $(brew --prefix) remote rm Linuxbrew
  2. Try git -C $(brew --prefix) fetch origin
  3. If that works, git -C $(brew --prefix) reset --hard 161e0bcdf

This should get you back to the head of SuperNEMO's brew. If the above work without error, then you can try:

$ brew update
$ brew rm bayeux falaise root5
$ brew install falaise

It's likely that additional formulae will need to be reinstalled, but let's try the above first.

cherylepatrick commented 7 years ago

Thanks for the help. I did all you suggested, but "brew install falaise" claimed falaise was already installed (even though I had just done the brew rm line). (It also said root5 was not installed when I tried to do the rm, but that is true, I uninstalled it earlier to stop myself getting error messages when I tried to run root 6). Do I need to brew uninstall falaise and bayeux too?

drbenmorgan commented 7 years ago

Ah, sorry, it's probably only uninstalled falaise/bayeux 3, so try

$ brew rm --force bayeux falaise root5

That should remove any and all versions, so should then allow the re-install of falaise.

cherylepatrick commented 7 years ago

Cool, now it is installing, wish me luck!

cherylepatrick commented 7 years ago

It ran suspiciously quickly, and now flsimulate is giving dyld: Library not loaded: @rpath/libCore.6.08.so Referenced from: /Users/cpatrick/CadfaelBrew/bin/flsimulate Reason: image not found Is that a sign of something else that needs a reinstall too?

cherylepatrick commented 7 years ago

Oh wait, that is a root library, maybe this is a problem with my LD_LIBRARY_PATH

drbenmorgan commented 7 years ago

Right, it looks like the issue has filtered through to other packages. I'd suggest doing:

$ brew reinstall root6 boost bayeux falaise

It is probably those that have caused the issue (I think geant4 will be o.k. as it hasn't been upgraded).

cherylepatrick commented 7 years ago

I tried all of those and it didn't work... now I get dyld: Library not loaded: @rpath/QtSvg.framework/Versions/5/QtSvg Referenced from: /Users/cpatrick/CadfaelBrew/bin/flsimulate Reason: image not found Abort trap: 6 I figured maybe that was QT so I reinstalled that as well. It took hours and made no difference. Any other suggestions? Sorry about this!

drbenmorgan commented 7 years ago

Don't apologise - good to get feedback!

I think, unfortunately, this means the whole stack is going to be affected, so I would recommend doing:

$ brew rm --force $(brew ls)
$ brew cadfael-bootstrap
$ brew install falaise

That's a complete rebuild, but think it's going to be needed...

cherylepatrick commented 7 years ago

Well it was drastic, but it seems like it worked. Yay! Thanks for your help, Ben!