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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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Problem to make install for bayeux #12

Closed miroslav-macko closed 7 years ago

miroslav-macko commented 7 years ago

Bug reports:

Hello!

I am trying to brew falaise and I managed to get rid of some problems up to some point when I am totally without any clue what might help. All the dependencies of falaise were installed until make install step for bayeux. Here is output I got:

[macko@borcluster1 Formula]$ brew install falaise ==> Installing falaise from supernemo-dbd/cadfael ==> Installing dependencies for supernemo-dbd/cadfael/falaise: supernemo-dbd/cadfael/bayeux ==> Installing supernemo-dbd/cadfael/falaise dependency: supernemo-dbd/cadfael/bayeux ==> Downloading https://files.warwick.ac.uk/supernemo/files/Cadfael/distfiles/Bayeux-2.1.0.tar.gz Already downloaded: /home/macko/.cache/Homebrew/bayeux-2.1.0.tar.gz ==> cmake .. -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/home/macko/Softver/linuxbrew/Cellar/bayeux/2.1.0_2 - ==> make install Last 15 lines from /home/macko/.cache/Homebrew/Logs/bayeux/02.make: from /home/macko/Softver/linuxbrew/include/boost/iostreams/detail/push.hpp:24, from /home/macko/Softver/linuxbrew/include/boost/iostreams/filtering_stream.hpp:19, etc....

I am also attaching file /home/macko/.cache/Homebrew/Logs/bayeux/02.make 02.make.txt

The problem seems to be in this part:

error "You need a ISO C conforming compiler to use the glibc headers"

I tried to google what might be the problem but it was not very helpful for me.

I hope you can help somehow.

Thank you,

Miroslav Macko

output of brew config:

[macko@borcluster1 ~]$ brew config HOMEBREW_VERSION: 1.1.10-34-g92bb61c50 ORIGIN: https://github.com/Linuxbrew/brew.git HEAD: 92bb61c506afd09388af2a391dd3f5998bdd4404 Last commit: 12 days ago Core tap ORIGIN: https://github.com/Linuxbrew/homebrew-core Core tap HEAD: acb11f825ac0b49d3b5420a2f7e90cf67e9bf440 Core tap last commit: 6 hours ago HOMEBREW_PREFIX: /home/macko/Softver/linuxbrew HOMEBREW_REPOSITORY: /home/macko/Softver/linuxbrew HOMEBREW_CELLAR: /home/macko/Softver/linuxbrew/Cellar HOMEBREW_BOTTLE_DOMAIN: https://linuxbrew.bintray.com CPU: 24-core 64-bit ivybridge Homebrew Ruby: 2.0.0-p648 => /home/macko/Softver/linuxbrew/Library/Homebrew/vendor/portable-ruby/2.0.0-p648/bin/ruby Clang: N/A Git: 2.12.0 => /home/macko/Softver/linuxbrew/bin/git Perl: /usr/bin/perl Python: /home/macko/Softver/linuxbrew/bin/python => /home/macko/Softver/linuxbrew/Cellar/python/2.7.13/bin/python2.7 Ruby: /usr/bin/ruby Java: 1.6.0_39 Kernel: Linux 2.6.32-573.26.1.el6.x86_64 x86_64 GNU/Linux OS: Scientific Linux release 6.4 (Carbon) Codename: Carbon OS glibc: 2.12 OS gcc: 4.4.7 Linuxbrew glibc: 2.19 Linuxbrew gcc: 5.3.0 Linuxbrew xorg: N/A

output of brew doctor:

[macko@borcluster1 Formula]$ brew doctor Your system is ready to brew.

drbenmorgan commented 7 years ago

I'd suspect this is down to using Linuxbrew's gcc and glibc. These aren't supported yet (I'll update the documents to reflect this), so the only solution is to remove your existing brew install (or create a new one) and do:

# ... Ensure you have don't have PATH or LD_LIBRARY_PATH pointing to any other locations...
$ git clone https://github.com/SuperNEMO-DBD/brew.git cadfaelbrew
$ cd cadfaelbrew
$ ./bin/brew cadfael-bootstrap
$ ./bin/brew install falaise
miroslav-macko commented 7 years ago

I tried to install this way and I got this message:

==> Checking for install of rpm 'openssl-devel': openssl-devel-1.0.1e-42.el6_7.4 Error: RPM 'ruby-irb.x86_64' is not installed Error: RPM 'HEP_OSlibs_SL6' is not installed Error: Yum Group 'Development tools' is not installed Error: RPMs 'HEP_OSlibs_SL6 ruby-irb.x86_64 ' are not installed on this system Error: Please run (or get your sysadmin to run):

install HEP_OSlibs_SL6 ruby-irb.x86_64 Error: Yum Groups ''Development tools'' are not installed on this system Error: Please run (or get your sysadmin to run): yum groupinstall 'Development tools' Error: System software check failed I am working in cluster system I cannot get sudo access to. Is there possiblity to install those 'Development tools' without sudo access? Maybe it is trivial issue but I was not able to do that. Thanks for any help.
drbenmorgan commented 7 years ago

As it says in the error message, contact support for your cluster and ask for the installation of the listed packages and groups. So for the base packages:

$ yum install ruby-irb.x86_64
$ yum groupinstall 'Development tools'

HEP_OSlibs is supplied by CERN, and there are instructions at https://twiki.cern.ch/twiki/bin/view/LCG/SL6DependencyRPM for installing this via the CERN repository and associated GPG key.

drbenmorgan commented 7 years ago

Closing issues more than 2 months old with no update, please reopen if required.