ADL: Build Vina form source code

Oleg Trott trott at scripps.edu
Thu Mar 27 10:54:35 PDT 2014


Hi

Those are warnings rather than errors. (And they are unavoidable, AFAIK)

On Wed, Mar 26, 2014 at 8:37 PM, tong <tongzhu9110 at gmail.com> wrote:
> Dear everyone,
>
>
> I want to build Vina from source code on my PC (CentOS 6.5 with Boost
> 1.41)
>
>
> The  Boost Libraries were installed in /usr/include/boost
>
>
> So I modified the Makefile
> in /Program/autodock_vina_1_1_2/build/linux/release to :
>
>
>
>
> BASE=/usr/local
> BOOST_VERSION=1_41
> BOOST_INCLUDE = /usr/include/boost
> C_PLATFORM=-static -pthread
> GPP=/usr/bin/g++
> C_OPTIONS= -O3 -DNDEBUG
> BOOST_LIB_VERSION=
>
> include ../../makefile_common
>
> However, when I typed make depend, there were so many errors:
>
>          make depend
> ln -sf `/usr/bin/g++ -print-file-name=libstdc++.a`
> rm -f dependencies_tmp dependencies_tmp.bak
> touch dependencies_tmp
> makedepend -f dependencies_tmp -Y
> -I ../../../src/lib ../../../src/lib/*.cpp ../../../src/tests/*.cpp ../../../src/design/*.cpp ../../../src/main/*.cpp ../../../src/split/*.cpp  ../../../src/tune/*.cpp
> makedepend: warning:  ../../../src/lib/cache.cpp, line 23: cannot find
> include file "algorithm"
> not in ../../../src/lib/algorithm
> makedepend: warning:  ../../../src/lib/cache.cpp, line 32: cannot find
> include file "boost/archive/text_oarchive.hpp"
> not in ../../../src/lib/boost/archive/text_oarchive.hpp
> makedepend: warning:  ../../../src/lib/cache.cpp, line 33: cannot find
> include file "boost/archive/text_iarchive.hpp"
> not in ../../../src/lib/boost/archive/text_iarchive.hpp
> makedepend: warning:  ../../../src/lib/cache.cpp, line 38: cannot find
> include file "boost/serialization/split_member.hpp"
> not in ../../../src/lib/boost/serialization/split_member.hpp
> makedepend: warning:  ../../../src/lib/cache.cpp, line 39: cannot find
> include file "boost/filesystem/fstream.hpp"
> not in ../../../src/lib/boost/filesystem/fstream.hpp
> makedepend: warning:  ../../../src/lib/cache.cpp, line 40: cannot find
> include file "boost/static_assert.hpp"
> not in ../../../src/lib/boost/static_assert.hpp
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/cache.h, line 26): cannot find include file
> "string"
> not in ../../../src/lib/string
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/common.h, line 26): cannot find include file
> "cassert"
> not in ../../../src/lib/cassert
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/common.h, line 27): cannot find include file
> "string"
> not in ../../../src/lib/string
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/common.h, line 28): cannot find include file
> "limits"
> not in ../../../src/lib/limits
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/common.h, line 29): cannot find include file
> "utility"
> not in ../../../src/lib/utility
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/common.h, line 30): cannot find include file
> "algorithm"
> not in ../../../src/lib/algorithm
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/common.h, line 31): cannot find include file
> "vector"
> not in ../../../src/lib/vector
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/common.h, line 32): cannot find include file
> "cmath"
> not in ../../../src/lib/cmath
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/common.h, line 33): cannot find include file
> "iostream"
> not in ../../../src/lib/iostream
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/common.h, line 34): cannot find include file
> "fstream"
> not in ../../../src/lib/fstream
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/common.h, line 35): cannot find include file
> "iomanip"
> not in ../../../src/lib/iomanip
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/common.h, line 36): cannot find include file
> "sstream"
> not in ../../../src/lib/sstream
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/common.h, line 37): cannot find include file
> "string"
> not in ../../../src/lib/string
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/common.h, line 39): cannot find include file
> "boost/serialization/vector.hpp"
> not in ../../../src/lib/boost/serialization/vector.hpp
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/common.h, line 40): cannot find include file
> "boost/serialization/base_object.hpp"
> not in ../../../src/lib/boost/serialization/base_object.hpp
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/common.h, line 41): cannot find include file
> "boost/filesystem/path.hpp"
> not in ../../../src/lib/boost/filesystem/path.hpp
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/array3d.h, line 26): cannot find include file
> "exception"
> not in ../../../src/lib/exception
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/grid_dim.h, line 26): cannot find include file
> "boost/array.hpp"
> not in ../../../src/lib/boost/array.hpp
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/model.h, line 26): cannot find include file
> "boost/optional.hpp"
> not in ../../../src/lib/boost/optional.hpp
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/file.h, line 26): cannot find include file
> "boost/filesystem/fstream.hpp"
> not in ../../../src/lib/boost/filesystem/fstream.hpp
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/conf.h, line 26): cannot find include file
> "boost/ptr_container/ptr_vector.hpp"
> not in ../../../src/lib/boost/ptr_container/ptr_vector.hpp
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/quaternion.h, line 26): cannot find include
> file "boost/math/quaternion.hpp"
> not in ../../../src/lib/boost/math/quaternion.hpp
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/quaternion.h, line 27): cannot find include
> file "boost/serialization/split_free.hpp"
> not in ../../../src/lib/boost/serialization/split_free.hpp
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/random.h, line 26): cannot find include file
> "boost/random.hpp"
> not in ../../../src/lib/boost/random.hpp
> makedepend: warning:  ../../../src/lib/cache.cpp
> (reading ../../../src/lib/matrix.h, line 26): cannot find include file
> "vector"
> not in ../../../src/lib/vector
> makedepend: warning:  ../../../src/lib/current_weights.cpp
> (reading ../../../src/lib/terms.h, line 26): cannot find include file
> "boost/ptr_container/ptr_vector.hpp"
> not in ../../../src/lib/boost/ptr_container/ptr_vector.hpp
> makedepend: warning:  ../../../src/lib/my_pid.cpp, line 26: cannot find
> include file "unistd.h"
> not in ../../../src/lib/unistd.h
> makedepend: warning:  ../../../src/lib/parallel_mc.cpp
> (reading ../../../src/lib/parallel.h, line 26): cannot find include file
> "vector"
> not in ../../../src/lib/vector
> makedepend: warning:  ../../../src/lib/parallel_mc.cpp
> (reading ../../../src/lib/parallel.h, line 30): cannot find include file
> "boost/optional.hpp"
> not in ../../../src/lib/boost/optional.hpp
> makedepend: warning:  ../../../src/lib/parallel_mc.cpp
> (reading ../../../src/lib/parallel.h, line 31): cannot find include file
> "boost/thread/thread.hpp"
> not in ../../../src/lib/boost/thread/thread.hpp
> makedepend: warning:  ../../../src/lib/parallel_mc.cpp
> (reading ../../../src/lib/parallel.h, line 32): cannot find include file
> "boost/thread/mutex.hpp"
> not in ../../../src/lib/boost/thread/mutex.hpp
> makedepend: warning:  ../../../src/lib/parallel_mc.cpp
> (reading ../../../src/lib/parallel.h, line 33): cannot find include file
> "boost/thread/condition.hpp"
> not in ../../../src/lib/boost/thread/condition.hpp
> makedepend: warning:  ../../../src/lib/parallel_mc.cpp
> (reading ../../../src/lib/parallel_progress.h, line 26): cannot find
> include file "boost/progress.hpp"
> not in ../../../src/lib/boost/progress.hpp
> makedepend: warning:  ../../../src/lib/parallel_mc.cpp
> (reading ../../../src/lib/parallel_progress.h, line 27): cannot find
> include file "boost/thread/mutex.hpp"
> not in ../../../src/lib/boost/thread/mutex.hpp
> makedepend: warning:  ../../../src/lib/parse_pdbqt.cpp, line 23: cannot
> find include file "fstream"
> not in ../../../src/lib/fstream
> makedepend: warning:  ../../../src/lib/parse_pdbqt.cpp, line 24: cannot
> find include file "sstream"
> not in ../../../src/lib/sstream
> makedepend: warning:  ../../../src/lib/parse_pdbqt.cpp, line 25: cannot
> find include file "cctype"
> not in ../../../src/lib/cctype
> makedepend: warning:  ../../../src/lib/parse_pdbqt.cpp, line 26: cannot
> find include file "boost/utility.hpp"
> not in ../../../src/lib/boost/utility.hpp
> makedepend: warning:  ../../../src/lib/parse_pdbqt.cpp, line 27: cannot
> find include file "boost/optional.hpp"
> not in ../../../src/lib/boost/optional.hpp
> makedepend: warning:  ../../../src/lib/parse_pdbqt.cpp, line 28: cannot
> find include file "boost/filesystem/fstream.hpp"
> not in ../../../src/lib/boost/filesystem/fstream.hpp
> makedepend: warning:  ../../../src/lib/parse_pdbqt.cpp, line 29: cannot
> find include file "boost/lexical_cast.hpp"
> not in ../../../src/lib/boost/lexical_cast.hpp
> makedepend: warning:  ../../../src/lib/parse_pdbqt.cpp
> (reading ../../../src/lib/convert_substring.h, line 26): cannot find
> include file "cctype"
> not in ../../../src/lib/cctype
> makedepend: warning:  ../../../src/lib/parse_pdbqt.cpp
> (reading ../../../src/lib/convert_substring.h, line 27): cannot find
> include file "boost/lexical_cast.hpp"
> not in ../../../src/lib/boost/lexical_cast.hpp
> makedepend: warning:  ../../../src/lib/random.cpp, line 23: cannot find
> include file "ctime"
> not in ../../../src/lib/ctime
> makedepend: warning:  cannot open "../../../src/tests/*.cpp"
> makedepend: warning:  cannot open "../../../src/design/*.cpp"
> makedepend: warning:  ../../../src/main/1.cpp, line 23: cannot find
> include file "iostream"
> not in ../../../src/lib/iostream
> makedepend: warning:  ../../../src/main/1.cpp, line 24: cannot find
> include file "string"
> not in ../../../src/lib/string
> makedepend: warning:  ../../../src/main/1.cpp, line 25: cannot find
> include file "exception"
> not in ../../../src/lib/exception
> makedepend: warning:  ../../../src/main/1.cpp, line 26: cannot find
> include file "vector"
> not in ../../../src/lib/vector
>
> Could you please tell me which mistake have I made?
>
> Thank you so much for your help!
>
>
> Tong
>
> ________________________________________________
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-- 
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com


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