Unable to successfully compile using Ubuntu 18.04.5 LTS

[Anonymous]

Hello,

I am currently unable to correclty compile Rossetta in a Ubuntu 18.04.5 LTS system.

The version I am currently using is Rosetta 3.12.

Then try to compile using with the following…

./scons.py -j 4 mode=release bin

The following terminal output and error are given:

./scons.py: line 1: XSym: command not found

./scons.py: line 2: 0029: command not found

./scons.py: line 3: 86dcd961cbe1608e8ebd368321edb1ba: command not found

scons: Reading SConscript files …

Running versioning script … Release package detected, using rosetta/main/.release.json to acquire version information…

Done. (0.0 seconds)

file ./options.dox being updated

file ./full-options-list.md being updated

Number of option files updated: 2

Total 4491 options.

Finished updating ResidueProperty code

— no changes needed

Finished updating VariantType code

— no changes needed

scons: done reading SConscript files.

scons: Building targets …

scons: `cppdb’ is up to date.

scons: `sqlite3′ is up to date.

scons: `cifparse’ is up to date.

scons: `libxml2′ is up to date.

scons: `libzmq’ is up to date.

scons: `ObjexxFCL’ is up to date.

scons: `utility’ is up to date.

scons: `numeric’ is up to date.

scons: `basic’ is up to date.

scons: `core.1′ is up to date.

scons: `core.2′ is up to date.

g++ -o build/src/release/linux/5.4/64/x86/gcc/7/default/core/pose/Pose.os -c -std=c++0x -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/pose/Pose.cc

In file included from src/core/io/mmtf/util.hh:26:0,

                 from src/core/io/mmtf/mmtf_writer.hh:25,

                 from src/core/pose/Pose.cc:62:

external/include/mmtf.hpp:3:1: error: invalid digit “9” in octal constant

 0914898a36b050854c3b418b5cd6d8e1

 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In file included from src/core/io/mmtf/mmtf_writer.hh:29:0,

                 from src/core/pose/Pose.cc:62:

external/include/mmtf.hpp:3:1: error: invalid digit “9” in octal constant

 0914898a36b050854c3b418b5cd6d8e1

 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In file included from src/core/io/mmtf/util.hh:26:0,

                 from src/core/io/mmtf/mmtf_writer.hh:25,

                 from src/core/pose/Pose.cc:62:

external/include/mmtf.hpp:1:1: error: ‘XSym’ does not name a type

 XSym

 ^~~~

In file included from src/core/io/mmtf/mmtf_writer.hh:29:0,

                 from src/core/pose/Pose.cc:62:

external/include/mmtf.hpp:1:1: error: ‘XSym’ does not name a type

 XSym

 ^~~~

src/core/pose/Pose.cc: In member function ‘void core::pose::Pose::dump_file(const string&) const’:

src/core/pose/Pose.cc:2056:13: error: ‘core::io::mmtf’ has not been declared

   core::io::mmtf::dump_mmtf( *this, file_name_string );

             ^~~~

src/core/pose/Pose.cc: In member function ‘void core::pose::Pose::dump_mmtf(const string&) const’:

src/core/pose/Pose.cc:2069:12: error: ‘core::io::mmtf’ has not been declared

  core::io::mmtf::dump_mmtf( *this, file_name );

            ^~~~

scons: *** [build/src/release/linux/5.4/64/x86/gcc/7/default/core/pose/Pose.os] Error 1

scons: building terminated because of errors.

 

How could I fixed this?

I would greatly appreciate your help. Thanks in advance.

 

[Anonymous]

I can’t say for certain, but it looks like you may have an issue with symlinks. Rosetta relies heavily on symlinks, and Ubuntu should be able to handle them fine. However, if you extracted the Rosetta distribution on a non-Linux operating system (e.g. Windows), or extracted it to a disk which was formatted for a non-Linux operating system, there may be issues with properly extracting the symlinks in the distributed repository.

In particular, it looks like your symlinks are being represented in an `XSym` format, rather than a native Linux one. I’m not too familiar with this format, but you would either need to extract the Rosetta distribution in such a way to use “native” Linux symlinks (e.g. re-extract the archive from within Ubuntu onto a Linux-native formatted disk), or find some way to get Ubuntu to transparently treat the XSym-like links like a native one.

[Anonymous]

Thank you very much! Your comment has been very helpful in order to solve my error. I re-downloaded the Rosetta files in a linux system and the compilation seems to work.

Again thanks a lot

[Author]

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