Installing revbayes on ubuntu

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Raimundo

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Oct 7, 2015, 2:50:10 PM10/7/15
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Dear all,
I have tried to compile  revbayes in ubuntu14.04. However  at end of process, I have the following message:

Linking CXX static library librb-parser.a
[ 99%] Built target rb-parser
make: *** [all] Error 2

Some idea for solve my issue? 
Kind regards,
raimundo

Sebastian Höhna

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Oct 8, 2015, 11:27:54 AM10/8/15
to Raimundo, revbayes-users
Dear Raimundo,

unfortunately I cannot tell you what is going wrong there. Could you please be a bit more specific what you did exactly? Did you try to compile the RevBayes source from the master branch on github using the build.sh script? And could you provide the lines before the few lines you showed? There should be a more specific error message somewhere in the compile output which tells you and us what specifically failed during the compilation.


Best,
Sebastian

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Raimundo

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Oct 8, 2015, 3:03:13 PM10/8/15
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Dear Sebastian, thank you for your response.
 I am using the version master on github, and compiling with build.sh. Below I have attached a screen of the compilation.  That is sufficient? 
Kind regards,
raimundo
rev_1.txt

Eva Drukker

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Oct 12, 2015, 7:39:41 AM10/12/15
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I have exactly the same problem when I try to install it on ubuntu. 
I followed the steps given in http://revbayes.github.io/installation.html up until "./build.sh" and after 99% it gives the same error. 
I hope you can find out what the error is!
Kind regards, 
Eva

Sebastian Höhna

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Oct 12, 2015, 11:39:11 AM10/12/15
to Eva Drukker, revbayes-users
Hi Raimundo and Eva,

I just pushed a fix to the master branch that should solve the problem. Please let me know if it still persists.

Best,
Sebastian

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Eva Drukker

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Oct 13, 2015, 4:11:49 AM10/13/15
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Hi Sebastian and Raimundo,

I removed everything and did the download again but unfortunately it still gave the same error after 99%. 
I did notice though that just after I started the compilation of ./build.sh it gave the following:
rm: cannot remove ‘./project-config.jam*’
But afterwards it continued the compilation so I don't know whether it might had anything to do with it at all.  

Best, Eva

Sebastian Höhna

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Oct 13, 2015, 11:31:12 AM10/13/15
to Eva Drukker, revbayes-users
Hi Eva, 

Could you send me the full error message that you get in the terminal?

Best 
Sebastian 

Andrés Parada

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Oct 13, 2015, 10:00:35 PM10/13/15
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I was just to post an issue but it might be better to piggyback in this question. Sorry if these issues are not related.
I couldn't install it under Ubuntu Vivid 15.04 using the source from github. Thanks in advance for your help. 

Using
~  ᐅ cmake --version / cmake version 3.3.2

I added the path to  the equivalent to profile in my machine ~/.zshrc 
export DYLD_LIBRARY_PATH=/home/andrelo/revbayes-master/boost_1_55_0/stage/lib:$DYLD_LIBRARY_PATH
export PATH=/home/andrelo/revbayes-master/projects/cmake:$PATH

I used the ./build.sh script. After the installation failed I tried the regenerate script. 

I tried to build again and got

~/revbayes-master/projects/cmake (master ✘)✭ ᐅ ./build.sh        
/home/andrelo/revbayes-master/projects/cmake
Building boost libraries
you can turn this of with argument "-boost false"
Building Boost.Build engine with toolset gcc... tools/build/v2/engine/bin.linuxx86_64/b2
Unicode/ICU support for Boost.Regex?... not found.
Generating Boost.Build configuration in project-config.jam...

Bootstrapping is done. To build, run:

    ./b2
    
To adjust configuration, edit 'project-config.jam'.
Further information:

   - Command line help:
     ./b2 --help
     
   - Getting started guide: 
     
   - Boost.Build documentation:

link.jam: No such file or directory

Building the Boost C++ Libraries.


Performing configuration checks

    - gcc visibility           : yes (cached)
    - long double support      : yes (cached)
    - has_icu builds           : yes (cached)
    - lockfree boost::atomic_flag : yes (cached)

Component configuration:

    - atomic                   : not building
    - chrono                   : not building
    - context                  : not building
    - coroutine                : not building
    - date_time                : building
    - exception                : not building
    - filesystem               : not building
    - graph                    : not building
    - graph_parallel           : not building
    - iostreams                : not building
    - locale                   : not building
    - log                      : not building
    - math                     : building
    - mpi                      : not building
    - program_options          : building
    - python                   : not building
    - random                   : not building
    - regex                    : building
    - serialization            : building
    - signals                  : building
    - system                   : not building
    - test                     : not building
    - thread                   : building
    - timer                    : not building
    - wave                     : not building

...patience...
...patience...
...patience...
...found 3670 targets...


The Boost C++ Libraries were successfully built!

The following directory should be added to compiler include paths:

    /home/andrelo/revbayes-master/boost_1_55_0

The following directory should be added to linker library paths:

    /home/andrelo/revbayes-master/boost_1_55_0/stage/lib


-- Boost version: 1.55.0
-- Found the following Boost libraries:
--   regex
--   program_options
--   system
--   thread
--   signals
--   date_time
--   serialization
Boost information:
  Boost_INCLUDE_DIRS: /home/andrelo/revbayes-master/boost_1_55_0
  Boost_LIBRARIES: /home/andrelo/revbayes-master/boost_1_55_0/stage/lib/libboost_regex.a;/home/andrelo/revbayes-master/boost_1_55_0/stage/lib/libboost_program_options.a;/home/andrelo/revbayes-master/boost_1_55_0/stage/lib/libboost_system.a;/home/andrelo/revbayes-master/boost_1_55_0/stage/lib/libboost_thread.a;/home/andrelo/revbayes-master/boost_1_55_0/stage/lib/libboost_signals.a;/home/andrelo/revbayes-master/boost_1_55_0/stage/lib/libboost_date_time.a;/home/andrelo/revbayes-master/boost_1_55_0/stage/lib/libboost_serialization.a
  Boost_LIBRARY_DIRS: /home/andrelo/revbayes-master/boost_1_55_0/stage/lib
-- Configuring done
-- Generating done
-- Build files have been written to: /home/andrelo/revbayes-master/projects/cmake
[  2%] Built target libs
[ 50%] Built target rb-parser
[ 50%] Building CXX object core/CMakeFiles/rb-core.dir/home/andrelo/revbayes-master/src/core/utils/RbFileManager.cpp.o
[ 50%] Building CXX object core/CMakeFiles/rb-core.dir/home/andrelo/revbayes-master/src/core/utils/RbException.cpp.o
[ 51%] Building CXX object core/CMakeFiles/rb-core.dir/home/andrelo/revbayes-master/src/core/utils/MpiUtilities.cpp.o
[ 51%] Building CXX object core/CMakeFiles/rb-core.dir/home/andrelo/revbayes-master/src/core/monitors/ExtendedNewickTreeMonitor.cpp.o
[ 51%] Building CXX object core/CMakeFiles/rb-core.dir/home/andrelo/revbayes-master/src/core/monitors/PosteriorPredictiveMonitor.cpp.o
/home/andrelo/revbayes-master/src/core/utils/RbFileManager.cpp: In member function ‘std::string RevBayesCore::RbFileManager::getFullFilePath() const’:
/home/andrelo/revbayes-master/src/core/utils/RbFileManager.cpp:284:77: error: ‘strncmp’ was not declared in this scope
     if(strncmp(filePath.c_str(), pathSeparator.c_str(), pathSeparator.size()) != 0)
                                                                             ^
[ 51%] Building CXX object core/CMakeFiles/rb-core.dir/home/andrelo/revbayes-master/src/core/monitors/ScreenMonitor.cpp.o
core/CMakeFiles/rb-core.dir/build.make:8222: recipe for target 'core/CMakeFiles/rb-core.dir/home/andrelo/revbayes-master/src/core/utils/RbFileManager.cpp.o' failed
make[2]: *** [core/CMakeFiles/rb-core.dir/home/andrelo/revbayes-master/src/core/utils/RbFileManager.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
/home/andrelo/revbayes-master/src/core/monitors/ScreenMonitor.cpp: In constructor ‘RevBayesCore::ScreenMonitor::ScreenMonitor(RevBayesCore::DagNode*, int, bool, bool, bool)’:
/home/andrelo/revbayes-master/src/core/monitors/ScreenMonitor.cpp:47:19: warning: converting to non-pointer type ‘long int’ from NULL [-Wconversion-null]
     enabled( true )
                   ^
/home/andrelo/revbayes-master/src/core/monitors/ScreenMonitor.cpp: In constructor ‘RevBayesCore::ScreenMonitor::ScreenMonitor(const std::vector<RevBayesCore::DagNode*>&, int, bool, bool, bool)’:
/home/andrelo/revbayes-master/src/core/monitors/ScreenMonitor.cpp:67:19: warning: converting to non-pointer type ‘long int’ from NULL [-Wconversion-null]
     enabled( true )
                   ^
CMakeFiles/Makefile2:179: recipe for target 'core/CMakeFiles/rb-core.dir/all' failed
make[1]: *** [core/CMakeFiles/rb-core.dir/all] Error 2
Makefile:83: recipe for target 'all' failed
make: *** [all] Error 2
~/revbayes-master/projects/cmake (master ✘)✭ ᐅ 
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Eva Drukker

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Oct 14, 2015, 4:02:44 AM10/14/15
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Hello all,

Here is the full error message I got when installing RevBayes on ubuntu 14.04.2 LTS:

[ 99%] /home/biosys/Applications/RevBayes_Mac/revbayes-master/src/core/utils/RbFileManager.cpp: In member function ‘std::string RevBayesCore::RbFileManager::getFullFilePath() const’:
/home/biosys/Applications/RevBayes_Mac/revbayes-master/src/core/utils/RbFileManager.cpp:284:77: error: ‘strncmp’ was not declared in this scope
     if(strncmp(filePath.c_str(), pathSeparator.c_str(), pathSeparator.size()) != 0)
                                                                             ^
Building CXX object revlanguage/CMakeFiles/rb-parser.dir/home/biosys/Applications/RevBayes_Mac/revbayes-master/src/revlanguage/utils/RlUtils.cpp.o
make[2]: *** [core/CMakeFiles/rb-core.dir/home/biosys/Applications/RevBayes_Mac/revbayes-master/src/core/utils/RbFileManager.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [core/CMakeFiles/rb-core.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
Linking CXX static library librb-parser.a
[ 99%] Built target rb-parser
make: *** [all] Error 2

I hope this helps! 
Kind regards, Eva

Andrés Parada

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Oct 14, 2015, 2:16:42 PM10/14/15
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Just a heads up, it worked now downloading the updated version from github. 
Thanks!
Message has been deleted

Raimundo

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Oct 14, 2015, 6:37:48 PM10/14/15
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I have downloaded the new version on github. Revbayes is working now.
THANKS
raimundo

Em quarta-feira, 7 de outubro de 2015 15:50:10 UTC-3, Raimundo escreveu:

Eva Drukker

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Oct 15, 2015, 3:41:04 AM10/15/15
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It works here too!! Hooray! Thank you!
Eva
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