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Building terminated because of errors,anyone can help me?

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Building terminated because of errors,anyone can help me?

the building terminate  because of errors,the output is:

external/boost_1_55_0/boost/mpl/vector/aux_/tag.hpp:17:10: fatal error: boost/mpl/aux_/config/typeof.hpp: No such file or directory
 #include <boost/mpl/aux_/config/typeof.hpp>
compilation terminated.
scons: *** [build/src/release/linux/4.4/64/x86/gcc/7/default/protocols/match/upstream/ProteinSCSampler.os] Error 1
scons: building terminated because of errors.

does anyone know how to fix it?  Thank you very much again!

Post Situation: 
Fri, 2018-09-21 01:16

The first thing I'd do is check if the file Rosetta/main/source/external/boost_1_55_0/boost/mpl/aux_/config/typeof.hpp exists.  It should in the regular Rosetta distribution. If it doesn't on your machine, there's something wrong with your download of Rosetta. I'd try re-downloading, and re-extracting the files.

If that file *does* exist, my guess is that there's some issue with your paths, potentially with boost directory finding. Sometimes there's issues where the system boost is used versus the Rosetta-distributed one. (Though that's curious, as it was able to find external/boost_1_55_0/boost/mpl/vector/aux_/tag.hpp no problem.)  Did you alter your tools/build/site.settings or tools/build/user.settings at all?

Fri, 2018-09-21 07:14

I didn't alter tools/build/site.settings or tools/build/user.settings and i have tried to building this many times,i got the error every time ,but the output were Similar but not identical,For example:

In file included from external/boost_1_55_0/boost/multi_index_container.hpp:25:0,
                 from external/boost_1_55_0/boost/graph/named_graph.hpp:20,
                 from external/boost_1_55_0/boost/graph/adjacency_list.hpp:45,
                 from external/boost_1_55_0/boost/graph/undirected_graph.hpp:10,
                 from src/core/chemical/ResidueGraphTypes.hh:37,
                 from src/core/chemical/ResidueType.hh:24,
                 from src/protocols/match/downstream/SecondaryMatcherToUpstreamResidue.hh:33,
                 from src/protocols/match/
external/boost_1_55_0/boost/mpl/contains.hpp:18:38: fatal error: boost/mpl/contains_fwd.hpp: No such file or directory
compilation terminated.
scons: *** [build/src/release/linux/4.4/64/x86/gcc/5.4/default/protocols/match/Matcher.os] Error 1

The problem is annoying ,can you try to fix it?Thank you very much again!

Fri, 2018-09-21 18:32

It's really hard to say what the issue is. The fact that you're getting different errors each time seems strange. Are you running with multiple processors? (That is with -j set to a number greater than one?) For debugging purposes, I'd run with -j1 until you get things fixed.

If you're running with `-j1` (or without `-j`), then the compilation should proceed the same way each time. That is, if you run it to error, then re-launch the command, you should get the same error on the same file. (And it should be the first Rosetta .cc file you compile (here which gives the error, as scons should pick up where it left off.)

If it's not -- if the re-launch of the compilation gives no errors on the prior command line but fails on a different file or with a different error -- then there's likely to be something wrong with your disk. For some reason when compiling your disk isn't properly reporting the presence of files, and is intermittently failing. I'd get your sysadmin to look at the hard drive you're putting Rosetta on.

If it is consistent, I'd double check that the file that it's reporting as being "No such file or directory" is present in your Rosetta/source directory. If it's not, then the issue is with your Rosetta installation -- for some reason when you extracted Rosetta from your downloaded tarball, it didn't get properly extracted. In that case, I'd recommend re-downloading and re-extracting Rosetta.

I'm highly doubtful about there being an issue with the include paths. But you can also check this. Take the g++ command which is printed when you run scons with -j1, and then run it directly from the commandline with `-Wp,-v` added right after the g++  (but don't add the backticks).  You should get some output like '#include <...> search starts here:' -- "external/boost_1_55_0/ " should be the second entry after that line.  The other thing you can do is take that g++ command and add `-H` after the g++ and `2>&1 | grep boost` at the very end. This should give a number of lines, but they all should contain "external/boost_1_55_0/", and there shouldn't be any "/usr/include" or "/usr/local/include" paths (or other such paths) there.


Mon, 2018-09-24 09:33


I have solved the problem successfully according to your method, just change '-j4' to '-j1',the building was done successfully.

Another problem confused me when i follow the tutorial about Controlling Input and Output in Rosetta .

If I want to calculate the energy of a refined PDB 1QYS,i should input

$> $ROSETTA3/bin/score_jd2.default.linuxgccrelease -in:file:s input_files/1qys.pdb

or just

$ROSETTA3/bin/score_jd2.default.linuxgccrelease -in:file:s input_files/1qys.pdb

The former code's output was 

-bash: /bin/score_jd2.default.linuxgccrelease: Permission denied

and the latter code's output was 

-bash: /bin/score_jd2.default.linuxgccrelease: No such file or directory

Can you help me about this ? Thank you very much for your answers!

Tue, 2018-09-25 09:12

In the tutorials, the "\$>" is standing in for a prompt. You shouldn't type it yourself, it just indicates what you should type.

Regarding the "/bin/score_jd2.default.linuxgccrelease: No such file or directory", that's indicating that you haven't set the ROSETTA3 environment variable. -- That's perfectly fine. Rosetta doesn't need it - I certainly don't have it set on my local machine. But if you don't have it set, you need to replace any occurance of \$ROSETTA3 with the actual path to Rosetta that you're using.  (Since we don't know where you installed Rosetta, we can't give the exact path in the tutorial, therefore we use \$ROSETTA3 as a stand-in.)

Tue, 2018-10-02 13:15