some “COMMAND ERROR” while installing rosetta2.1.0

This topic has 2 replies, 3 voices, and was last updated 12 years, 9 months ago by Anonymous.

Viewing 2 reply threads

Author

Posts
- March 22, 2012 at 5:57 am #1208
  Anonymous
  I am trying to install Rosetta++2.1.0
  and I changed the options.settings file to be compatible with gccc 4.5 which is in my my CYGWIN
  but I am getting the following big error.
  
  I will be very grateful if somebody could suggest a solution:
  
  ERROR :
  cygwin warning:
  MS-DOS style path detected: C:Documents and SettingsAll UsersApplication Da tascons/site_scons
  Preferred POSIX equivalent is: /cygdrive/c/Documents and Settings/All Users/Ap plication Data/scons/site_scons
  CYGWIN environment variable option “nodosfilewarning” turns off this warning.
  Consult the user’s guide for more details about POSIX paths:
  http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
  scons: Reading SConscript files …
  
  scons: warning: The Options class is deprecated; use the Variables class instead .
  File “/home/user/rosetta/rosetta++/tools/build/setup.py”, line 32,in setup_build_options
  scons: warning: The EnumOption() function is deprecated; use the EnumVariable() function instead.
  File “/home/user/rosetta/rosetta++/tools/build/setup.py”, line 40, in setup_build_options
  
  scons: warning: The ListOption() function is deprecated; use the ListVariable() function instead.
  File “/home/user/rosetta/rosetta++/tools/build/setup.py”, line 48, in setup_build_options
  
  scons: warning: The build_dir keyword has been deprecated; use the variant_dir k eyword instead.
  File “/home/user/rosetta/rosetta++/SConscript”, line 19, in
  
  scons: warning: The env.Copy() method is deprecated; use the env.Clone() method instead.
  File “/home/user/rosetta/rosetta++/src/SConscript.src”, line 86, in
  
  scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
  File “/home/user/rosetta/rosetta++/SConscript”, line 19, in
  
  scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
  File “/home/user/rosetta/rosetta++/SConscript”, line 19, in
  
  scons: warning: The build_dir keyword has been deprecated; use the variant_dir k eyword instead.
  File “/home/user/rosetta/rosetta++/SConscript”, line 19, in
  
  scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
  File “/home/user/rosetta/rosetta++/SConscript.rosetta++”, line 20, in
  Traceback (most recent call last):
  File “/home/user/rosetta/rosetta++/SConstruct”, line 101, in main
  SConscript(“SConscript.rosetta++”, “build”)
  File “/usr/lib/scons-2.1.0/SCons/Script/SConscript.py”, line 614, in __call__
  return method(*args, **kw)
  File “/usr/lib/scons-2.1.0/SCons/Script/SConscript.py”, line 551, in SConscrip t
  return _SConscript(self.fs,**subst_kw) *files,
  File “/usr/lib/scons-2.1.0/SCons/Script/SConscript.py”, line 260, in _SConscri pt
  exec _file_ in call_stack[-1].globals
  File “/home/user/rosetta/rosetta++/SConscript.rosetta++”, line 20, in
  build_dir = build_path, duplicate = False)
  File “/usr/lib/scons-2.1.0/SCons/Script/SConscript.py”, line 614, in __call__
  return method(*args, **kw)
  File “/usr/lib/scons-2.1.0/SCons/Script/SConscript.py”, line 551, in SConscriptreturn _SConscript(self.fs, *files,**subst_kw)
  File “/usr/lib/scons-2.1.0/SCons/Script/SConscript.py”, line 260, in _SConscri pt
  exec _file_ in call_stack[-1].globals
  File “/home/user/rosetta/rosetta++/SConscript.src.rosetta++”, line 198, in
  command % os.path.join(“build”, “src”, build.platform, “rosetta++”))
  NameError: name ‘command’ is not defined
  scons: done reading SConscript files.
  scons: Building targets …
  g++ -o build/src/release/cygwin/1.7/32/x86/gcc/numeric/constants.o -c -std=c++98 -pipe -ffor-scope -W -Wall -pedantic -fno-exceptions -malign-double -march=pent ium4 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s – Wno-unused-variable -std=c99 -pipe -ffor-scope -W -Wall -pedantic -fno-exception s -malign-double -march=pentium4 -O3 -ffast-math -funroll-loops -finline-functio ns -finline-limit=20000 -s -Wno-unused-variable -DNDEBUG -Isrc -Iexternal/includ e -Isrc/platform/cygwin/1.7/32/x86/gcc -Isrc/platform/cygwin/1.7/32/x86 -Isrc/pl atform/cygwin/1.7/32 -Isrc/platform/cygwin/1.7 -Isrc/platform/cygwin -I/usr/loca l/include -I/usr/include src/numeric/constants.cc
  /usr/lib/gcc/i686-pc-cygwin/4.5.3/cc1plus.exe: error while loading shared librar ies: cygcloog-0.dll: cannot open shared object file: No such file or directory
  scons: *** [build/src/release/cygwin/1.7/32/x86/gcc/numeric/constants.o] Error 1
  scons: building terminated because of errors.
  
  Please advise ASAP
- March 22, 2012 at 2:56 pm #6838
  Anonymous
  The best advice I can give you is not to try to compile R2.1 on cygwin. Generally, if things are misconfigured for cygwin, none of the developers really know how to help. Do you have a unix/linux OS available?
- March 22, 2012 at 4:00 pm #6839
  Anonymous
  As Steven says, the general recommendations are 1) not to compile on cygwin if you can avoid it and 2) not to use Rosetta++ if you can avoid it. (Broadly speaking, only use Rosetta++ for replicating results done previously with Rosetta++, and for those rare protocols not yet transitioned to Rosetta3. All of the development and almost all of the usage in Rosetta labs is now with Rosetta3.)
  
  That said, your issues look to be in lines 193-198 of /home/user/rosetta/rosetta++/SConscript.src.rosetta++ — there’s looks to be an if/else clause between an os type of “linux”, “macos” and “windows” – my guess is that cygwin is using something like “cygwin” for the os type. If you really need to compile it under cygwin, try adding “cygwin” to the “linux” and “macos” line (hopefully cygwin is Unix-like enough for that to work – try adding it to the “windows” line if it doesn’t.) You might want to also add something like “print ‘OS TYPE STRING:’, build.options.os” to the line before the if statement to double check what cygwin is calling itself (it’s Python, so indentation matters. Match the indentation of the surrounding lines.)
Author

Posts

Viewing 2 reply threads

You must be logged in to reply to this topic.