Rosetta Commons

March 2, 2011 at 10:35 am #5107

Anonymous

Hi there,

I am having some trouble building/installing the rosetta 3.2 and the problem can be summarized as follows:

My OS is Ubuntu 10.10, on inspiron 6400, dual core 1.8, 2GB RAM

I installed Ubuntu 10.10

then i installed the pyshell from the software manager

I also installed gcc ver4.1 (sudo apt-get install gcc-4.1)

I installed scons (sudo apt-get install scons)

I installed g++ (sudo apt-get install g++)

I also installed svn (sudo apt-get install svn)

Then i tried building rosetta-3.2 (sudo scons bin mode release)

I got:
bomalk@ubuntu://media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source$ scons bin mode=release
scons: Reading SConscript files …
svn: ‘.’ is not a working copy

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File “/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/SConscript”, line 40, in
scons: done reading SConscript files.
scons: Building targets …
g++ -o build/src/release/linux/2.6/32/x86/gcc/apps/public/AbinitioRelax.o -c -std=c++98 -pipe -ffor-scope -W -Wall -pedantic -Wno-long-long -malign-double -march=pentium4 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/32/gcc -Isrc/platform/linux/32 -Isrc/platform/linux -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/apps/public/AbinitioRelax.cc

this ended in the error:
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.

I tried to look it up and then installed other versions of gcc ver=4.1

Then tried sudo scons bin mode=release cxx=gcc cxx_ver=4.1

i got the same error, so i went to the basic.settings and added
“cc” : “gcc-4.1”,
“cxx” : “g++-4.1”
which made my file look like this

# be C99? Are there portability issues?
“cc” : [ “std=c99” ],
“cxx” : [ “std=c++98” ],
“compile” : [ “pipe”, “ffor-scope” ],
“cc” : “gcc-4.1”,
“cxx” : “g++-4.1”,
# By default, warn as much as possible.
“warn” : [ “W”, “Wall”, “pedantic”,

the i ran scons again
scons bin mode=release cxx=gcc cxx_ver=4.1
but then i got another error,

abomalk@ubuntu:/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source$ scons bin mode=release cxx=gcc cxx_ver=4.1
scons: Reading SConscript files …
Traceback (most recent call last):
File “/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/SConstruct”, line 139, in main
build = SConscript(“tools/build/setup.py”)
File “/usr/lib/scons/SCons/Script/SConscript.py”, line 614, in __call__
return method(*args, **kw)
File “/usr/lib/scons/SCons/Script/SConscript.py”, line 551, in SConscript
return _SConscript(self.fs, *files, **subst_kw)
File “/usr/lib/scons/SCons/Script/SConscript.py”, line 260, in _SConscript
exec _file_ in call_stack[-1].globals
File “/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/tools/build/setup.py”, line 411, in
build = setup()
File “/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/tools/build/setup.py”, line 403, in setup
build.settings = setup_build_settings(build.options)
File “/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/tools/build/setup.py”, line 227, in setup_build_settings
settings += [ BuildSettingsCombined(id, supported[id]) ]
File “/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/tools/build/settings.py”, line 326, in __init__
setattr(self, name, BuildSettings(value))
File “/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/tools/build/settings.py”, line 195, in __init__
self.flags = BuildFlags(**self.flags)
File “/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/tools/build/settings.py”, line 175, in __init__
assert type(value) is list, “Parameters of BuildFlags must be lists”
AssertionError: Parameters of BuildFlags must be lists
scons: done reading SConscript files.
scons: Building targets …
scons: `bin’ is up to date.
scons: done building targets.

What should i do next?

Reply To: Build Error, ubuntu 10.10, scons 2.0, python 2.6.6 and gcc 4.4.5, truncation