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compile Rosetta 3.9 for rifdock

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compile Rosetta 3.9 for rifdock
#1

Hi,

I ran into some error when compiling Rosetta 3.9. I ran the command scons -j4 mode=release bin.

Here is the error.

In file included from src/utility/options/FileVectorOption.hh:24,
                 from src/utility/options/OptionCollection.hh:35,
                 from src/utility/options/OptionCollection.cc:17:
src/utility/options/keys/FileVectorOptionKey.hh: In instantiation of 'utility::options::VectorOption_T_<K, T>& utility::options::VectorOption_T_<K, T>::operator=(const utility::options::VectorOption_T_<K, T>&) [with K = utility::options::FileVectorOptionKey; T = utility::file::FileName]':
src/utility/options/FileVectorOption.hh:38:7:   required from here
src/utility/options/keys/FileVectorOptionKey.hh:35:7: warning: implicitly-declared 'utility::options::VectorOptionKey& utility::options::VectorOptionKey::operator=(const utility::options::VectorOptionKey&)' is deprecated [-Wdeprecated-copy]
   35 | class FileVectorOptionKey :
      |       ^~~~~~~~~~~~~~~~~~~
In file included from src/utility/options/keys/BooleanVectorOptionKey.hh:23,
                 from src/utility/options/BooleanVectorOption.hh:24,
                 from src/utility/options/OptionCollection.hh:30,
                 from src/utility/options/OptionCollection.cc:17:
src/utility/options/keys/VectorOptionKey.hh:53:2: note: because 'utility::options::VectorOptionKey' has user-provided 'utility::options::VectorOptionKey::VectorOptionKey(const utility::options::VectorOptionKey&)'
   53 |  VectorOptionKey( VectorOptionKey const & key ) :
      |  ^~~~~~~~~~~~~~~
In file included from src/utility/options/BooleanVectorOption.hh:23,
                 from src/utility/options/OptionCollection.hh:30,
                 from src/utility/options/OptionCollection.cc:17:
src/utility/options/VectorOption_T_.hh:156:9: note: synthesized method 'utility::options::FileVectorOptionKey& utility::options::FileVectorOptionKey::operator=(const utility::options::FileVectorOptionKey&)' first required here
  156 |    key_ = option.key_;
      |    ~~~~~^~~~~~~~~~~~~
In file included from src/utility/options/PathVectorOption.hh:24,
                 from src/utility/options/OptionCollection.hh:36,
                 from src/utility/options/OptionCollection.cc:17:
src/utility/options/keys/PathVectorOptionKey.hh: In instantiation of 'utility::options::VectorOption_T_<K, T>& utility::options::VectorOption_T_<K, T>::operator=(const utility::options::VectorOption_T_<K, T>&) [with K = utility::options::PathVectorOptionKey; T = utility::file::PathName]':
src/utility/options/PathVectorOption.hh:38:7:   required from here
src/utility/options/keys/PathVectorOptionKey.hh:35:7: warning: implicitly-declared 'utility::options::VectorOptionKey& utility::options::VectorOptionKey::operator=(const utility::options::VectorOptionKey&)' is deprecated [-Wdeprecated-copy]
   35 | class PathVectorOptionKey :
      |       ^~~~~~~~~~~~~~~~~~~
In file included from src/utility/options/keys/BooleanVectorOptionKey.hh:23,
                 from src/utility/options/BooleanVectorOption.hh:24,
                 from src/utility/options/OptionCollection.hh:30,
                 from src/utility/options/OptionCollection.cc:17:
src/utility/options/keys/VectorOptionKey.hh:53:2: note: because 'utility::options::VectorOptionKey' has user-provided 'utility::options::VectorOptionKey::VectorOptionKey(const utility::options::VectorOptionKey&)'
   53 |  VectorOptionKey( VectorOptionKey const & key ) :
      |  ^~~~~~~~~~~~~~~
In file included from src/utility/options/BooleanVectorOption.hh:23,
                 from src/utility/options/OptionCollection.hh:30,
                 from src/utility/options/OptionCollection.cc:17:
src/utility/options/VectorOption_T_.hh:156:9: note: synthesized method 'utility::options::PathVectorOptionKey& utility::options::PathVectorOptionKey::operator=(const utility::options::PathVectorOptionKey&)' first required here
  156 |    key_ = option.key_;
      |    ~~~~~^~~~~~~~~~~~~

May I ask how to solve this? I just downloaded the software and unzipped it so I cannot think of any reason why it does not work. Thank you!

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Thu, 2022-11-17 06:34
szhang

Rosetta 3.9 is now 4-5 years old. The warnings you post are due to compilers changing in the mean time to not allow something they used to allow. (If you use an older compiler from 2017 or so, then it would not have those warnings.)

That said, those should just be warnings, and not errors. Compilation should still continue after those messages get printed. If you run scons until it finishes, and then re-run `scons -j1 mode=release bin` What's the full log that gets printed? It may be there's some other error which is getting printed which isn't captured in the snippet you posted.

Thu, 2022-11-17 08:02
rmoretti

Thank you for the reply! When I reran it, it just said completed immediately. I guess it means the compilation is fine? However when I installed rifdock successfully, I cannot run $RIFDOCK/build/apps/rosetta/rifgen @input/rifgen.flag > rifgen.log 2>&1. There is an error message saying 'Unable to open file: /home/me/rifdock/rifdock_rosetta/main/database/chemical/residue_type_sets/fa_standard/residue_types.txt'. I feel like the program is trying to locate its rosetta to a default path instead of the one I claimed. I already ran 'export CMAKE_ROSETTA_PATH=xxx' and 'export CMAKE_FINAL_ROSETTA_PATH=xxx' to redefine the path. Do you happen to know what else I can do to help it find the right path? Thank you!

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Fri, 2022-11-18 07:05
szhang

Note that with CMAKE variables, you'll need to set those prior to executing the cmake build step. (And depending on what they are, you may need to do a clean build as well.)

I'm not 100% on RIFdock and how it finds Rosetta, but generally Rosetta finds the database path relative to the executable. Failing that, you can specify the path to the database location with the `-database` command line option (which may or may not be obeyed with rifgen), or you can set the ROSETTA3_DB environment variable.

Fri, 2022-11-18 08:36
rmoretti