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scons: building terminated because of errors.

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scons: building terminated because of errors.

when compling ./ -j<number_of_processors_to_use> mode=release bin command,


src/protocols/antibody/ error: 'StructureID' has not been declared
  623 |         StructureID struct_id,
      |         ^~~~~~~~~~~
scons: *** [build/src/release/linux/5.15/64/x86/gcc/11/default/protocols/antibody/clusters/CDRClusterFeatures.os] Error 1
scons: *** [build/src/release/linux/5.15/64/x86/gcc/11/default/protocols/antibody/AntibodyFeatures.os] Error 1
scons: building terminated because of errors.

Are there any possible reasons for that?

Any help will be appreciated.

Post Situation: 
Mon, 2022-07-18 20:26

Is that the first error you see? I'd recommend re-running the scons command, but with -j1. (It should pick up where it left off, so it shouldn't take that much time.) That should result in a cleaner error message log. You'll want to look at the first messages which get printed out, as that will show more where the original error is. From what I'm seeing in the code, the StructureID is probably not the original error, but is showing up because an earlier error is confusing the compiler.

P.S. Which version of Rosetta are you compiling?

Tue, 2022-07-19 09:08

I am also having the same issue - outside of the 'g++: warning: switch '-ffor-scope' is no longer supported' messages, the first warning message I get is:

In file included from src/protocols/features/FeaturesReporterCreator.hh:21,
                 from src/protocols/antibody/AntibodyFeaturesCreator.hh:18,
                 from src/protocols/antibody/
src/protocols/features/FeaturesReporter.fwd.hh:27:14: error: 'uint64_t' in namespace 'std' does not name a type; did you mean 'wint_t'?

I've tried the command with -j3, -j1 and no -j at all. I can upload a dump of the messages that it put in the console if you would like?


I'm trying the most recent version of Rosetta (3.13)


Is there anything that I can do to get this to compile correctly?

Tue, 2022-07-19 10:28

I've also just tried on a fresh extraction of the files - The types of error I get are:

  • src/protocols/features/FeaturesReporter.fwd.hh:27:14: error: 'uint64_t' in namespace 'std' does not name a type; did you mean 'wint_t'?
  • src/protocols/features/FeaturesReporter.hh:99:17: error: 'StructureID' has not been declared
  • src/protocols/antibody/AntibodyFeatures.hh:104:27: error: 'protocols::features::StructureID' has not been declared
  • scons: *** [build/src/release/linux/5.15/64/x86/gcc/11/default/protocols/antibody/AntibodyFeaturesCreator.os] Error 1
  • src/protocols/features/util.hh:79:9: error: 'StructureID' was not declared in this scope
  • src/protocols/features/util.hh:80:42: error: expected primary-expression before 'db_session'
  • src/protocols/features/util.hh:81:1: error: expression list treated as compound expression in initializer [-fpermissive]
  • src/protocols/features/util.hh:83:29: error: template argument 1 is invalid
  • scons: *** [build/src/release/linux/5.15/64/x86/gcc/11/default/protocols/antibody/AntibodyFeatures.os] Error 1


These numbers (in the earlier errors)

I've attached a full txt file with the output of the command.

File attachments: 
Tue, 2022-07-19 10:55

"'uint64_t' in namespace 'std' does not name a type" is the issue you're running up against, and all the other errors are stemming from that one. I'm not sure what platform you're compiling on, but it sounds like it's having problems with that standard C++ type. (Which, admittedly, is optional for compilers to support, but should be availible on pretty much all modern systems.)

The first thing I'd do is add the line

#include <cstdint>

to the top of source/src/protocols/features/FeaturesReporter.fwd.hh (after the other #include line). Hopefully that should fix things.

If it doesn't, you can try changing the line

typedef std::uint64_t StructureID;


typedef unsigned long long StructureID;

That should get things to compile, though the features reporter framework may or may not work exactly how you expect. (But that shouldn't matter much if you don't use it, which you probably won't unless you know you want it.)

Thu, 2022-07-21 08:35