installation on OSX

Question

installation on OSX

Closed this issue 6 years ago · 22 comments

I am trying to used Biopython to compute some DSSP values for a bunch of pdbs (https://biopython.org/DIST/docs/api/Bio.PDB.DSSP%27-module.html).
I seem to struggle to install DSSP though.
Naively, following the instructions and standard ways of installing on a unix system, I went ahead and cloned the repository:

git clone https://github.com/cmbi/xssp.git   
cd xssp
./configure    
make    
make install

The error I get is:

./configure: No such file or directory

Not really sure how to trouble shoot this.

Answer 1 · 2018-06-15T11:49:12.000Z

Dear user, you can run the autogen.sh script to create the configure script. But you need to have the autoconf, automake and autotools-dev packages installed for that. I'll adjust this in the readme file too. Greetings, Coos

…

________________________________ Van: ppxasjsm <notifications@github.com> Verzonden: vrijdag 15 juni 2018 13:31 Aan: cmbi/xssp CC: Subscribed Onderwerp: [cmbi/xssp] installation on OSX (#94) I am trying to used Biopython to compute some DSSP values for a bunch of pdbs (https://biopython.org/DIST/docs/api/Bio.PDB.DSSP%27-module.html). I seem to struggle to install DSSP though. Naively, following the instructions and standard ways of installing on a unix system, I went ahead and cloned the repository: git clone https://github.com/cmbi/xssp.git cd xssp ./configure make make install The error I get is: ./configure: No such file or directory Not really sure how to trouble shoot this. - You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#94>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AFN1sz93ApyGBSHayhOU5_NtAA1IWfxLks5t85stgaJpZM4Upa5f>. Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

Answer 2 · 2018-09-20T18:29:46.000Z

Hi
I am trying to install xssp-3.0.2 on macOS High Sierra (10.13.6) using clang (Apple LLVM version 10.0.0 (clang-1000.11.45.2)) and get the following fatal error:
./src/primitives-3d.h:15:10: fatal error: 'boost/tr1/tuple.hpp' file not found

I am using boost 1.68.0 compiled with clang and installed using the instructions provided here (https://solarianprogrammer.com/2018/08/07/compiling-boost-gcc-clang-macos/). The boost lib and include files are in:

/usr/local/boost-1.68.0/lib/
/usr/local/boost-1.68.0/include/boost/

The commands used to configure and compile xssp-3.0.2 are:

./autogen.sh 
./configure --with-boost=/usr/local/boost-1.68.0/
make

The indicated missing boost file boost/tr1/tuple.hpp is really in /usr/local/boost-1.68.0/include/boost/tuple/tuple.hpp
-rw-r--r--@ 1 root wheel 1.9K Sep 20 13:34 /usr/local/boost-1.68.0/include/boost/tuple/tuple.hpp

The following have been added to my .profile file:

export DYLD_LIBRARY_PATH=/usr/local/boost-1.68.0/lib:$DYLD_LIBRARY_PATH
export BOOST_ROOT=/usr/local/boost-1.68.0
export BOOST_LIB_DIR=/usr/local/boost-1.68.0/lib
export BOOST_INC_DIR=/usr/local/boost-1.68.0/include

Any suggestions?

Answer 3 · 2018-09-27T09:30:53.000Z

I've just created a new release (3.0.3) without the tr1 library. I replaced it with features from the c++ standard library. If you build this version, you should no longer get the error about that one missing header.

https://github.com/cmbi/xssp/releases

Greetings!

Answer 4 · 2018-10-10T11:41:17.000Z

Hi,
I'm trying to install xssp-3.0.3 on Mac OS X Mojave
I have used the following commands with success:

./autogen.sh 
./configure

now running make gives a number of errors.
Here I have included only the first since the following might be a consequence of the first.

In file included from src/dssp.cpp:11:
./src/mas.h:44:9: error: keyword is hidden by macro definition [-Werror,-Wkeyword-macro]

Any ideas how to get around this?

Thanx, Claus

Answer 5 · 2018-10-10T11:59:01.000Z

This is a problem occuring more often for mac users. To fix it, remove the lines 43, 44, 45 from mas.h that say:

#ifndef nullptr
#define nullptr NULL
#endif

Answer 6 · 2018-10-10T12:05:39.000Z

Thanks a lot,
That took care of most of it, however I still have one error left:

src/structure.cpp:38:3: error: unused variable 'kSSBridgeDistance' [-Werror,-Wunused-const-variable]
  kSSBridgeDistance = 3.0,

Any more tricks?
Once again thanks for the help, it is most appreciated.

Answer 7 · 2018-10-10T12:09:06.000Z

The compiler is right, this value isn't used. So you can remove this line. I will omit it from the next release.

Answer 8 · 2018-10-10T12:28:54.000Z

Hi again,

Sorry to be a nuisance but I got a new error later in the progress:

src/fetchdbrefs.cpp:12:10: fatal error: 'zeep/xml/document.hpp' file not found
#include <zeep/xml/document.hpp>

Best, Claus

Answer 9 · 2018-10-10T13:39:41.000Z

Hi,
I successfully compiled libzeep on macOS High Sierra (10.13.6) by largely modifying libzeep's makefile manually. I used the latest boost 1.687.

BOOST_LIB_SUFFIX   = -mt
BOOST              = /usr/local
BOOST_LIB_DIR       = $(BOOST:%=%/lib)
BOOST_INC_DIR       = $(BOOST:%=%/include)

PREFIX              ?= /Users/hogehoge/apps
LIBDIR              ?= $(PREFIX)/lib
INCDIR              ?= $(PREFIX)/include
MANDIR              ?= $(PREFIX)/man/man3
DOCDIR              ?= $(PREFIX)/share/libzeep

BOOST_LIBS          = system thread filesystem regex math_c99 random
BOOST_LIBS          := $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX))
LIBS                = $(BOOST_LIBS) stdc++ m pthread
LDFLAGS             += $(BOOST_LIB_DIR:%=-L%) $(LIBS:%=-l%) -g

VERSION_MAJOR       = 3.0
VERSION_MINOR       = 3
VERSION             = $(VERSION_MAJOR).$(VERSION_MINOR)
DIST_NAME           = libzeep-$(VERSION)
SO_NAME             = libzeep.dylib.$(VERSION_MAJOR)
LIB_NAME            = $(SO_NAME).$(VERSION_MINOR)

and

lib: libzeep.a # libzeep.so

libzeep.a: $(OBJECTS)
        ar rc $@ $(OBJECTS)
        ranlib $@
#       ld -r -o $@ $(OBJECTS)

$(LIB_NAME): $(OBJECTS)
        $(CXX) -o $@ -dynamiclib -install_name $(SO_NAME) $(LDFLAGS) $(OBJECTS)

$(SO_NAME): $(LIB_NAME)
        ln -fs $(LIB_NAME) $@

libzeep.dylib: $(SO_NAME)
        ln -fs $(LIB_NAME) $@

# assuming zeep-test is build when install was not done already
zeep-test: obj/zeep-test.o libzeep.a
        $(CXX) $(BOOST_INC_DIR:%=-I%) -o $@ -I. $^ $(LDFLAGS) -lboost_date_time -lboost_regex

install-libs: libzeep.dylib
        install -d $(LIBDIR)
        install $(LIB_NAME) $(LIBDIR)/$(LIB_NAME)
        ln -fs $(LIB_NAME) $(LIBDIR)/$(SO_NAME)
        #strip --strip-unneeded $(LIBDIR)/$(LIB_NAME)

Additionally, for src/preforked-http-server.cpp, I replaced native_type with native_handle_type to comply with the latest boost specification. I also changed line 296 *fdptr = socket.native_handle();.

Then, make -j4 && make install-libs generated libzeep.dylib.3.0.3.

Using this libzeep.dylib.3.0.3, I also tried compilation of xssp-3.0.3.

./autogen.sh
 ./configure --prefix=/Users/hogehoge/xssp/3.0.3 CC=/usr/bin/gcc CXX=/usr/bin/g++ LDFLAGS=-L/Users/hogehoge/apps/libzeep CPPFLAGS='-I/Users/hogehoge/apps/libzeep -Wunused-const-variable'

LDFLAGS and CPPFLAGS is set to avoid the error. 'zeep/xml/document.hpp' file not found.

mkdssp was successfully generated by make -j8 mkdssp (but mkdssp doesn't require libzeep inherently... ). However, make -j4 to compile all programs failed with this error message.

$ make -j4
/Applications/Xcode.app/Contents/Developer/usr/bin/make  all-am
/usr/bin/g++  -g -O2  -L/Users/hogehoge/apps/libzeep -o mkdssp src/dssp.o src/iocif.o src/mas.o src/mkdssp.o src/primitives-3d.o src/structure.o src/utils.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread-mt -lpthread
/usr/bin/g++  -g -O2  -L/Users/hogehoge/apps/libzeep -o mkhssp src/blast.o src/dssp.o src/fasta.o src/fetchdbrefs.o src/hssp-nt.o src/iocif.o src/mas.o src/matrix.o src/mkhssp.o src/primitives-3d.o src/progress.o src/structure.o src/utils.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread-mt -lpthread -lboost_timer -lzeep
Undefined symbols for architecture x86_64:
  "MCounter::operator=(long long)", referenced from:
      MProgress::Progress(long long) in progress.o
  "MCounter::operator+=(long long)", referenced from:
      MProgress::Consumed(long long) in progress.o
  "MCounter::operator++(int)", referenced from:
      boost::detail::thread_data<HSSP::MProfile::Process(std::__1::basic_istream<char, std::__1::char_traits<char> >&, float, float, unsigned int, unsigned int)::$_1>::run() in hssp-nt.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [mkhssp] Error 1
make: *** [all] Error 2

Any ideas to solve it?

Answer 10 · 2018-10-11T07:15:55.000Z

Looks like you are building with 64bit architecture, right?

Did you build boost with that same architecture also?

Answer 11 · 2018-10-11T07:24:22.000Z

Hi again,

Sorry to be a nuisance but I got a new error later in the progress:
src/fetchdbrefs.cpp:12:10: fatal error: 'zeep/xml/document.hpp' file not found
#include <zeep/xml/document.hpp>
Best, Claus

Do you have libzeep installed? If not, then the configure step will only give a warning. However, libzeep is required to build mkhssp. If you only need mkdssp, the you should be able to build that without libzeep just fine.

Answer 12 · 2018-10-11T07:39:17.000Z

Yes that's true and I do only need mkdssp 👍

Answer 13 · 2018-10-11T10:33:28.000Z

Looks like you are building with 64bit architecture, right?

Did you build boost with that same architecture also?

I installed boost 1.67 by brew install boost without any options. I believe the boost libraries are 64bit architecture.

test_fasta, test_readpdb, and hsspconv were succesfully compiled, but mkhssp failed. When compiling the three programs, errors related to boost didn't occur.

/usr/bin/g++  -g -O2  -L/Users/hogehoge/apps/libzeep -o test_fasta src/fasta.o src/iocif.o src/mas.o src/primitives-3d.o src/structure.o src/utils.o tests/test_fasta.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread-mt -lpthread -lboost_unit_test_framework-mt
/usr/bin/g++  -g -O2  -L/Users/hogehoge/apps/libzeep -o test_readpdb src/fasta.o src/iocif.o src/mas.o src/primitives-3d.o src/structure.o src/utils.o tests/test_readpdb.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread-mt -lpthread -lboost_unit_test_framework-mt
/usr/bin/g++  -g -O2  -L/Users/hogehoge/apps/libzeep -o hsspconv src/hssp-convert-3to1.o src/hsspconv.o src/utils.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread-mt -lpthread
/usr/bin/g++  -g -O2  -L/Users/hogehoge/apps/libzeep -o test_conv src/hssp-convert-3to1.o src/utils.o src/mas.o tests/test_conv.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread-mt -lpthread -lboost_unit_test_framework-mt
/usr/bin/g++  -g -O2  -L/Users/hogehoge/apps/libzeep -o mkhssp src/blast.o src/dssp.o src/fasta.o src/fetchdbrefs.o src/hssp-nt.o src/iocif.o src/mas.o src/matrix.o src/mkhssp.o src/primitives-3d.o src/progress.o src/structure.o src/utils.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread-mt -lpthread -lboost_timer -lzeep
Undefined symbols for architecture x86_64:
  "MCounter::operator=(long long)", referenced from:
      MProgress::Progress(long long) in progress.o
  "MCounter::operator+=(long long)", referenced from:
      MProgress::Consumed(long long) in progress.o
  "MCounter::operator++(int)", referenced from:
      boost::detail::thread_data<HSSP::MProfile::Process(std::__1::basic_istream<char, std::__1::char_traits<char> >&, float, float, unsigned int, unsigned int)::$_1>::run() in hssp-nt.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [mkhssp] Error 1
make[1]: *** Waiting for unfinished jobs....
make: *** [all] Error 2

The compiler was Apple LLVM 10.0.0.

$ /usr/bin/g++ --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 10.0.0 (clang-1000.11.45.2)
Target: x86_64-apple-darwin17.7.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

Answer 14 · 2018-10-11T11:23:13.000Z

Could you try running that same clang command with '-v', so that we can see the invocation?

Answer 15 · 2018-10-11T11:29:14.000Z

Would this be okay?

$ /usr/bin/g++ -g -O2  -L/Users/hogehoge/apps/libzeep -o mkhssp src/blast.o src/dssp.o src/fasta.o src/fetchdbrefs.o src/hssp-nt.o src/iocif.o src/mas.o src/matrix.o src/mkhssp.o src/primitives-3d.o src/progress.o src/structure.o src/utils.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread-mt -lpthread -lboost_timer -lzeep -v

Apple LLVM version 10.0.0 (clang-1000.11.45.2)
Target: x86_64-apple-darwin17.7.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
 "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld" -demangle -lto_library /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/libLTO.dylib -dynamic -arch x86_64 -macosx_version_min 10.13.0 -o mkhssp -L/Users/hogehoge/apps/libzeep src/blast.o src/dssp.o src/fasta.o src/fetchdbrefs.o src/hssp-nt.o src/iocif.o src/mas.o src/matrix.o src/mkhssp.o src/primitives-3d.o src/progress.o src/structure.o src/utils.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread-mt -lpthread -lboost_timer -lzeep -lc++ -lSystem /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/10.0.0/lib/darwin/libclang_rt.osx.a
Undefined symbols for architecture x86_64:
  "MCounter::operator=(long long)", referenced from:
      MProgress::Progress(long long) in progress.o
  "MCounter::operator+=(long long)", referenced from:
      MProgress::Consumed(long long) in progress.o
  "MCounter::operator++(int)", referenced from:
      boost::detail::thread_data<HSSP::MProfile::Process(std::__1::basic_istream<char, std::__1::char_traits<char> >&, float, float, unsigned int, unsigned int)::$_1>::run() in hssp-nt.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)

Answer 16 · 2018-10-11T12:28:35.000Z

You could try to build in a different architecture. If you configure with:

./configure "CXXFLAGS=-m32" "CFLAGS=-m32" "LDFLAGS=-m32"

And then run 'make' again.

Answer 17 · 2018-10-11T14:29:51.000Z

Thank you for your suggestion. However, the setting didn't work well...

./configure --prefix=/usr/local/Cellar/xssp/3.0.3 CC=/usr/bin/gcc CXX=/usr/bin/g++ LDFLAGS='-L/Users/hogehoge/apps/libzeep -m32' CPPFLAGS='-I/Users/hogehoge/apps/libzeep -Wunused-const-variable -m32' CXXFLAGS=-m32 CFLAGS=-m32

and make clean ; make -j4

...Skip...

       /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep -Wunused-const-variable -m32  -m32 -MT src/dssp.o -MD -MP -MF $depbase.Tpo -c -o src/dssp.o src/dssp.cpp &&\
        mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/mkdssp.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep -Wunused-const-variable -m32  -m32 -MT src/mkdssp.o -MD -MP -MF $depbase.Tpo -c -o src/mkdssp.o src/mkdssp.cpp &&\
        mv -f $depbase.Tpo $depbase.Po
/usr/bin/g++  -m32  -L/Users/hogehoge/apps/libzeep -m32 -o test_fasta src/fasta.o src/iocif.o src/mas.o src/primitives-3d.o src/structure.o src/utils.o tests/test_fasta.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread-mt -lpthread -lboost_unit_test_framework-mt
ld: warning: The i386 architecture is deprecated for macOS (remove from the Xcode build setting: ARCHS)
ld: warning: ld: warning: ld: warning: ignoring file /usr/local/lib/libboost_date_time-mt.dylib, file was built for x86_64 which is not the architecture being linked (i386): /usr/local/lib/libboost_date_time-mt.dylibignoring file /usr/local/lib/libboost_filesystem.dylib, file was built for x86_64 which is not the architecture being linked (i386): /usr/local/lib/libboost_filesystem.dylibignoring file /usr/local/lib/libboost_iostreams-mt.dylib, file was built for x86_64 which is not the architecture being linked (i386): /usr/local/lib/libboost_iostreams-mt.dylib


ld: warning: ignoring file /usr/local/lib/libboost_system.dylib, file was built for x86_64 which is not the architecture being linked (i386): /usr/local/lib/libboost_system.dylibld: warning:
ld: warning: ignoring file /usr/local/lib/libboost_program_options-mt.dylib, file was built for x86_64 which is not the architecture being linked (i386): /usr/local/lib/libboost_program_options-mt.dylibignoring file /usr/local/lib/libboost_regex-mt.dylib, file was built for x86_64 which is not the architecture being linked (i386): /usr/local/lib/libboost_regex-mt.dylib

ld: warning: ignoring file /usr/local/lib/libboost_thread-mt.dylib, file was built for x86_64 which is not the architecture being linked (i386): /usr/local/lib/libboost_thread-mt.dylib
ld: warning: ignoring file /usr/local/lib/libboost_unit_test_framework-mt.dylib, file was built for x86_64 which is not the architecture being linked (i386): /usr/local/lib/libboost_unit_test_framework-mt.dylib
Undefined symbols for architecture i386:
  "boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)", referenced from:
      bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, unsigned long, int>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long const&, char const*, int const&, char const*) in test_fasta.o
  "boost::this_thread::interruption_point()", referenced from:
      boost::condition_variable::wait(boost::unique_lock<boost::mutex>&) in structure.o
      void boost::condition_variable_any::wait<boost::unique_lock<boost::mutex> >(boost::unique_lock<boost::mutex>&) in structure.o
  "boost::this_thread::disable_interruption::disable_interruption()", referenced from:
      boost::shared_mutex::lock_shared() in structure.o
      boost::shared_mutex::lock() in structure.o
  "boost::this_thread::disable_interruption::~disable_interruption()", referenced from:
      boost::shared_mutex::lock_shared() in structure.o
      boost::shared_mutex::lock() in structure.o
  "boost::detail::thread_data_base::~thread_data_base()", referenced from:
      boost::detail::thread_data<boost::_bi::bind_t<void, boost::_mfi::mf1<void, MProtein, std::__1::vector<MResidue*, std::__1::allocator<MResidue*> > const&>, boost::_bi::list2<boost::_bi::value<MProtein*>, boost::reference_wrapper<std::__1::vector<MResidue*, std::__1::allocator<MResidue*> > > > > >::~thread_data() in structure.o
      boost::detail::thread_data<boost::_bi::bind_t<void, boost::_mfi::mf2<void, MProtein, buffer<MResidue*, 100u>&, std::__1::vector<MResidue*, std::__1::allocator<MResidue*> > const&>, boost::_bi::list3<boost::_bi::value<MProtein*>, boost::reference_wrapper<buffer<MResidue*, 100u> >, boost::reference_wrapper<std::__1::vector<MResidue*, std::__1::allocator<MResidue*> > const> > > >::~thread_data() in structure.o
  "boost::detail::get_current_thread_data()", referenced from:
      boost::detail::interruption_checker::interruption_checker(_opaque_pthread_mutex_t*, _opaque_pthread_cond_t*) in structure.o
  "boost::system::generic_category()", referenced from:
      boost::system::error_category::std_category::equivalent(int, std::__1::error_condition const&) const in fasta.o
      boost::system::error_category::std_category::equivalent(std::__1::error_code const&, int) const in fasta.o
      boost::system::error_category::std_category::equivalent(int, std::__1::error_condition const&) const in iocif.o
      boost::system::error_category::std_category::equivalent(std::__1::error_code const&, int) const in iocif.o
      boost::system::error_category::std_category::equivalent(int, std::__1::error_condition const&) const in structure.o
      boost::system::error_category::std_category::equivalent(std::__1::error_code const&, int) const in structure.o
      boost::thread_exception::thread_exception(int, char const*) in structure.o
      ...
  "boost::thread::join_noexcept()", referenced from:
      boost::thread::join() in structure.o
  "boost::thread::native_handle()", referenced from:
      boost::thread::get_id() const in structure.o
  "boost::thread::hardware_concurrency()", referenced from:
      MProtein::CalculateAccessibilities(std::__1::vector<MResidue*, std::__1::allocator<MResidue*> > const&) in structure.o
  "boost::thread::start_thread_noexcept()", referenced from:
      boost::thread::start_thread() in structure.o
  "boost::thread::detach()", referenced from:
      boost::thread::~thread() in structure.o
  "boost::unit_test::unit_test_main(bool (*)(), int, char**)", referenced from:
      _main in test_fasta.o
  "boost::unit_test::unit_test_log_t::set_checkpoint(boost::unit_test::basic_cstring<char const>, unsigned long, boost::unit_test::basic_cstring<char const>)", referenced from:
      test_mkhssp_suite::test_read_proteins_from_fasta_single_invoker() in test_fasta.o
      test_mkhssp_suite::test_read_proteins_from_fasta_single::test_method() in test_fasta.o
      test_mkhssp_suite::test_read_proteins_from_fasta_multiple_invoker() in test_fasta.o
      test_mkhssp_suite::test_read_proteins_from_fasta_multiple::test_method() in test_fasta.o
  "boost::unit_test::framework::master_test_suite()", referenced from:
      init_unit_test() in test_fasta.o
  "boost::unit_test::test_case::test_case(boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long, boost::function<void ()> const&)", referenced from:
      boost::unit_test::make_test_case(boost::function<void ()> const&, boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long) in test_fasta.o
  "boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long, boost::unit_test::decorator::collector&)", referenced from:
      ___cxx_global_var_init.2 in test_fasta.o
  "boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)", referenced from:
      ___cxx_global_var_init.5 in test_fasta.o
      ___cxx_global_var_init.12 in test_fasta.o
  "boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(int)", referenced from:
      ___cxx_global_var_init.18 in test_fasta.o
  "boost::unit_test::ut_detail::normalize_test_case_name(boost::unit_test::basic_cstring<char const>)", referenced from:
      boost::unit_test::make_test_case(boost::function<void ()> const&, boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long) in test_fasta.o
  "boost::thread::joinable() const", referenced from:
      boost::thread_group::join_all() in structure.o
  "typeinfo for boost::detail::thread_data_base", referenced from:
      typeinfo for boost::detail::thread_data<boost::_bi::bind_t<void, boost::_mfi::mf1<void, MProtein, std::__1::vector<MResidue*, std::__1::allocator<MResidue*> > const&>, boost::_bi::list2<boost::_bi::value<MProtein*>, boost::reference_wrapper<std::__1::vector<MResidue*, std::__1::allocator<MResidue*> > > > > > in structure.o
      typeinfo for boost::detail::thread_data<boost::_bi::bind_t<void, boost::_mfi::mf2<void, MProtein, buffer<MResidue*, 100u>&, std::__1::vector<MResidue*, std::__1::allocator<MResidue*> > const&>, boost::_bi::list3<boost::_bi::value<MProtein*>, boost::reference_wrapper<buffer<MResidue*, 100u> >, boost::reference_wrapper<std::__1::vector<MResidue*, std::__1::allocator<MResidue*> > const> > > > in structure.o
  "vtable for boost::detail::thread_data_base", referenced from:
      boost::detail::thread_data_base::thread_data_base() in structure.o
  NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
  "vtable for boost::unit_test::unit_test_log_t", referenced from:
      boost::unit_test::unit_test_log_t::unit_test_log_t() in test_fasta.o
  NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
ld: symbol(s) not found for architecture i386
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [test_fasta] Error 1
make[1]: *** Waiting for unfinished jobs....
make: *** [all] Error 2

Answer 18 · 2018-10-12T08:04:35.000Z

OK, forget that! Just compile with 64bit architecture.

Try replacing line 9 of src/progress.h:

#if defined(__linux__)

should become:

#if defined(__linux__) || defined(__APPLE__)

Answer 19 · 2018-10-13T06:59:14.000Z

I changed src/progress.h as you wrote and then tried compilation. However, another issue occurred. When using Apple LLVM 10.0.0 compiler,

$ ./configure --prefix=/Users/hogehoge/xssp/3.0.3 CC=/usr/bin/gcc CXX=/usr/bin/g++ LDFLAGS=-L/Users/hogehoge/apps/libzeep CPPFLAGS='-I/Users/hogehoge/apps/libzeep'

$ make clean ; make -j4
test -z "mkdssp mkhssp hsspconv test_fasta test_conv test_readpdb" || rm -f mkdssp mkhssp hsspconv test_fasta test_conv test_readpdb
test -z "mtrx/matrices.h" || rm -f mtrx/matrices.h
rm -f *.o
rm -f src/*.o
rm -f tests/*.o
perl mtrx/mkmat_h.pl mtrx/
/Applications/Xcode.app/Contents/Developer/usr/bin/make  all-am
depbase=`echo src/iocif.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/iocif.o -MD -MP -MF $depbase.Tpo -c -o src/iocif.o src/iocif.cpp &&\
        mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/mas.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/mas.o -MD -MP -MF $depbase.Tpo -c -o src/mas.o src/mas.cpp &&\
        mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/primitives-3d.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/primitives-3d.o -MD -MP -MF $depbase.Tpo -c -o src/primitives-3d.o src/primitives-3d.cpp &&\
        mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/structure.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/structure.o -MD -MP -MF $depbase.Tpo -c -o src/structure.o src/structure.cpp &&\
        mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/utils.o -MD -MP -MF $depbase.Tpo -c -o src/utils.o src/utils.cpp &&\
        mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/blast.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/blast.o -MD -MP -MF $depbase.Tpo -c -o src/blast.o src/blast.cpp &&\
        mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/fasta.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/fasta.o -MD -MP -MF $depbase.Tpo -c -o src/fasta.o src/fasta.cpp &&\
        mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/fetchdbrefs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/fetchdbrefs.o -MD -MP -MF $depbase.Tpo -c -o src/fetchdbrefs.o src/fetchdbrefs.cpp &&\
        mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/hssp-nt.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/hssp-nt.o -MD -MP -MF $depbase.Tpo -c -o src/hssp-nt.o src/hssp-nt.cpp &&\
        mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/matrix.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/matrix.o -MD -MP -MF $depbase.Tpo -c -o src/matrix.o src/matrix.cpp &&\
        mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/mkhssp.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\

        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/mkhssp.o -MD -MP -MF $depbase.Tpo -c -o src/mkhssp.o src/mkhssp.cpp &&\
        mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/progress.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/progress.o -MD -MP -MF $depbase.Tpo -c -o src/progress.o src/progress.cpp &&\
        mv -f $depbase.Tpo $depbase.Po
src/hssp-nt.cpp:1085:25: error: cannot increment value of type 'MCounter' (aka 'boost::detail::atomic_count')
        uint64 next = ix++;
                      ~~^
depbase=`echo src/hssp-convert-3to1.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/hssp-convert-3to1.o -MD -MP -MF $depbase.Tpo -c -o src/hssp-convert-3to1.o src/hssp-convert-3to1.cpp &&\
        mv -f $depbase.Tpo $depbase.Po
1 error generated.
make[1]: *** [src/hssp-nt.o] Error 1
make[1]: *** Waiting for unfinished jobs....
src/progress.cpp:183:23: error: no viable overloaded '+='
    (mImpl->mConsumed += inConsumed) >= mImpl->mMax and
     ~~~~~~~~~~~~~~~~ ^  ~~~~~~~~~~
src/progress.cpp:194:23: error: no viable overloaded '='
    (mImpl->mConsumed = inProgress) >= mImpl->mMax and
     ~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~
/usr/local/include/boost/smart_ptr/detail/atomic_count_std_atomic.hpp:51:20: note: candidate function not viable: no known conversion
      from 'int64' (aka 'long long') to 'const boost::detail::atomic_count' for 1st argument
    atomic_count & operator=(atomic_count const &);
                   ^
2 errors generated.
make[1]: *** [src/progress.o] Error 1

the Apple clang compiler couldn't compile them.

I found that this issue didn't occur when compiling with GNU compiler 6 or 8 installed by Homebrew. However, there remains some boost issue...

        mv -f $depbase.Tpo $depbase.Po
depbase=`echo tests/test_readpdb.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
        /usr/local/bin/g++-6 -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT tests/test_readpdb.o -MD -MP -MF $depbase.Tpo -c -o tests/test_readpdb.o tests/test_readpdb.cpp &&\
        mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/dssp.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
        /usr/local/bin/g++-6 -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/dssp.o -MD -MP -MF $depbase.Tpo -c -o src/dssp.o src/dssp.cpp &&\
        mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/mkdssp.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
        /usr/local/bin/g++-6 -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/mkdssp.o -MD -MP -MF $depbase.Tpo -c -o src/mkdssp.o src/mkdssp.cpp &&\
        mv -f $depbase.Tpo $depbase.Po
/usr/local/bin/g++-6  -g -O2  -L/Users/hogehoge/apps/libzeep -o test_fasta src/fasta.o src/iocif.o src/mas.o src/primitives-3d.o src/structure.o src/utils.o tests/test_fasta.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread-mt -lpthread -lboost_unit_test_framework-mt
Undefined symbols for architecture x86_64:
  "boost::unit_test::ut_detail::normalize_test_case_name[abi:cxx11](boost::unit_test::basic_cstring<char const>)", referenced from:
      boost::unit_test::make_test_case(boost::function<void ()> const&, boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long) in test_fasta.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[1]: *** [test_fasta] Error 1
make[1]: *** Waiting for unfinished jobs....
make: *** [all] Error 2

Answer 20 · 2018-10-15T08:38:40.000Z

Could you try building boost with the gnu compiler also?

Otherwise, try removing lines 11,12,13,16,17,18,19 from progress.h, saying:

#if defined(__INTEL_COMPILER_BUILD_DATE) || \
    (defined(__GNUC__) && (__GNUC__ > 4 || \
                           ( __GNUC__ == 4 && __GNUC_MINOR__ >= 6)))

#else
#include <boost/detail/atomic_count.hpp>
typedef boost::detail::atomic_count        MCounter;
#endif

And build with your clang compiler.

Answer 21 · 2018-10-16T02:54:00.000Z

Great! mkhssp finally worked well on macOS High Sierra !
As cbaakman suggested, I modified some lines in src/progress.h like this

#pragma once

#if defined(__linux__) || defined(__APPLE__)

#include <atomic>
typedef std::atomic<int64>  MCounter;

#else

struct MCounter
{
  MCounter(int64 inValue) : m_value(inValue) {}

      operator int64() const          { return m_value; }

  int64  operator++(int);
  int64  operator+=(int64 inValue);
  int64  operator=(int64 inValue);

  int64  m_value;
};
#endif

Then, ./configure --prefix=/Users/hogehoge/xssp/3.0.3 CC=/usr/bin/gcc CXX=/usr/bin/g++ LDFLAGS=-L/Users/hogehoge/apps/libzeep CPPFLAGS=-I/Users/hogehoge/apps/libzeep, make clean ; make -j4

/usr/bin/g++  -g -O2  -L/Users/hogehoge/apps/libzeep -o test_fasta src/fasta.o src/iocif.o src/mas.o src/primitives-3d.o src/structure.o src/utils.o tests/test_fasta.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread-mt -lpthread -lboost_unit_test_framework-mt
/usr/bin/g++  -g -O2  -L/Users/hogehoge/apps/libzeep -o test_readpdb src/fasta.o src/iocif.o src/mas.o src/primitives-3d.o src/structure.o src/utils.o tests/test_readpdb.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread-mt -lpthread -lboost_unit_test_framework-mt
/usr/bin/g++  -g -O2  -L/Users/hogehoge/apps/libzeep -o hsspconv src/hssp-convert-3to1.o src/hsspconv.o src/utils.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread-mt -lpthread
/usr/bin/g++  -g -O2  -L/Users/hogehoge/apps/libzeep -o test_conv src/hssp-convert-3to1.o src/utils.o src/mas.o tests/test_conv.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread-mt -lpthread -lboost_unit_test_framework-mt
/usr/bin/g++  -g -O2  -L/Users/hogehoge/apps/libzeep -o mkhssp src/blast.o src/dssp.o src/fasta.o src/fetchdbrefs.o src/hssp-nt.o src/iocif.o src/mas.o src/matrix.o src/mkhssp.o src/primitives-3d.o src/progress.o src/structure.o src/utils.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread-mt -lpthread -lboost_timer -lzeep
/usr/bin/g++  -g -O2  -L/Users/hogehoge/apps/libzeep -o mkdssp src/dssp.o src/iocif.o src/mas.o src/mkdssp.o src/primitives-3d.o src/structure.o src/utils.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread-mt -lpthread
[hogehoge@MyMacbook-pro] $ ln -s /Users/hogehoge/apps/libzeep/libzeep.dylib.3.0 . # include libzeep dynamic library
[hogehoge@MyMacbook-pro] $ ./mkdssp -h
mkdssp 3.0.1 options:
  -h [ --help ]         Display help message
  -i [ --input ] arg    Input PDB file (.pdb) or mmCIF file (.cif/.mcif),
                        optionally compressed by gzip (.gz) or bzip2 (.bz2)
  -o [ --output ] arg   Output file, optionally compressed by gzip (.gz) or
                        bzip2 (.bz2). Use 'stdout' to output to screen
  -v [ --verbose ]      Verbose output
  --version             Print version and citation info
  -d [ --debug ] arg    Debug level (for even more verbose output)


Examples:

To calculate the secondary structure for the file 1crn.pdb and
write the result to a file called 1crn.dssp, you type:

  ./mkdssp -i 1crn.pdb -o 1crn.dssp
[hogehoge@MyMacbook-pro] $ ./mkhssp -h
mkhssp options:
  -h [ --help ]           Display help message
  -i [ --input ] arg      PDB ID or input PDB file (.pdb), mmCIF file
                          (.cif/.mcif), or fasta file (.fa/.fasta), optionally
                          compressed by gzip (.gz) or bzip2 (.bz2)
  -o [ --output ] arg     Output file, optionally compressed by gzip (.gz) or
                          bzip2 (.bz2). Use 'stdout' to output to screen
  -d [ --databank ] arg   Databank to use (can be specified multiple times)
  -a [ --threads ] arg    Number of threads (default is maximum)
  --min-length arg        Minimal chain length (default = 25)
  --fragment-cutoff arg   Minimal alignment length as fraction of chain length
                          (default = 0.75)
  -O [ --gap-open ] arg   Gap opening penalty (default is 30.0)
  -E [ --gap-extend ] arg Gap extension penalty (default is 2.0)
  --threshold arg         Homology threshold adjustment (default = 0.05)
  -m [ --max-hits ] arg   Maximum number of hits to include (default = 5000)
  --fetch-dbrefs          Fetch DBREF records for each UniProt ID
  -v [ --verbose ]        Verbose mode
  --version               Show version number and citation info

I really appreciate your taking time. I hope that the installation log will contribute to other macOS users.

Answer 22 · 2018-10-16T07:11:50.000Z

I guess we'll just always use the std::atomic, since this is supported by default for c++11 anyway.