[phenixbb] Compilation problem rosetta MR on Fedora 10

[Eugene Valkov]

Hi Martin,

I had encountered an issue with building Rosetta 3.2.1 on Ubuntu
11.04, specifically that SCons could not compile it because it used
gcc 4.1 libraries, whereas there was gcc 4.4 installed.

Could you check what version of gcc you have installed on your Fedora box?

If it is the compiler issue then there are some workarounds documented
on Rosetta forums:

https://www.rosettacommons.org/node/2274


These worked for me, but you have to hack around in code a bit to make
it happen.

HTH,
Eugene


> On 15 December 2011 13:08, Martin Moche <Martin.Moche at ki.se> wrote:
>> Dear Phenix Users,
>>
>> I am trying to compile rosetta mr on my fedora 10 computer:
>> http://www.phenix-online.org/documentation/mr_rosetta.htm#anch35
>>
>> Compared to the instructions
>> % tar xzf rosetta3.2_Bundles.tgz
>>
>> did not work for me, instead I run
>> % tar xvf rosetta3.2_Bundles.tgz
>>
>> and subsequently
>> % tar xvf BioTools-3.3.tgz
>> % tar xvf protocol_capture-3.3.tgz
>> etc etc
>>
>> From the rosetta_source directory as an ordinary user (not root) I run:
>> % python scons.py -j2 bin mode=release
>>
>> The compilation runs for a while but finally I got the termination message
>> below.
>>
>> What should I try next?
>>
>> Best regards,
>> Martin
>>
>> #################### my computer info ##################
>>
>> daffy-mochma 183% scons --version
>> SCons by Steven Knight et al.:
>>     script: v1.0.0.d20080826.r3315, 2008/08/26 11:30:08, by scons on
>> scons-dev
>>     engine: v1.0.0.d20080826.r3315, 2008/08/26 11:30:08, by scons on
>> scons-dev
>> Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 The SCons
>> Foundation
>>
>> daffy-mochma 104% uname -a
>> Linux daffy 2.6.27.41-170.2.117.fc10.i686 #1 SMP Thu Dec 10 11:00:29 EST
>> 2009 i686 i686 i386 GNU/Linux
>>
>> daffy-mochma 105% python --version
>> Python 2.5.2
>>
>>
>>
>> ############# termination message #############################
>>
>> g++ -o build/src/release/linux/2.6/32/x86/gcc/libutility.so
>> -Wl,-rpath=/net/fileserver/xtal/rosetta3.3_bundles/rosetta_source/build/external/release/linux/2.6/32/x86/gcc/
>> -shared
>> build/src/release/linux/2.6/32/x86/gcc/utility/pointer/ReferenceCount.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/pointer/ReferenceCountMI_.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/options/OptionCollection.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/options/mpi_stderr.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/tag/Tag.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/sql_database/DatabaseSessionManager.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/boinc/boinc_util.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/io/icstream.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/io/izstream.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/io/ocstream.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/io/ozstream.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/options/keys/OptionKeys.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/excn/Exceptions.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/file/file_sys_util.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/file/FileName.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/file/gzip_util.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/file/PathName.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/basic_sys_util.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/string_util.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/heap.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/integer_mapping.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/mpi_util.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/exit.os
>> build/src/release/linux/2.6/32/x86/gcc/utility/LexicographicalIterator.os
>> -Llib -Lexternal/lib -Lbuild/src/release/linux/2.6/32/x86/gcc -Lsrc
>> -Lbuild/external/release/linux/2.6/32/x86/gcc -Lexternal -L/usr/local/lib
>> -L/usr/lib -lObjexxFCL -lz -lcppdb -lsqlite3
>> /usr/bin/ld: cannot find -lz
>> collect2: ld returned 1 exit status
>> scons: *** [build/src/release/linux/2.6/32/x86/gcc/libutility.so] Error 1
>> scons: building terminated because of errors.
>>
>>
>> Martin Moche, Ph.D.
>> Head of Protein Crystallography
>> Karolinska Institutet
>> MBB/PSF
>> Scheeles väg 2
>> 171 77 Stockholm
>> Sweden
>> phone:   +46-8-524 868 43
>> mobile: +46-73-322 93 27
>> fax:     +46-8-524 868 68
>> email:  Martin.Moche at ki.se
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>


-- 
Eugene Valkov, D.Phil.
MRC Career Development Fellow

Division of Structural Studies
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH

email: evalkov at mrc-lmb.cam.ac.uk
tel: +44 (0)1223 402261