Package: ChemmineOB

Version: 1.22.0

Command: rm -rf ChemmineOB.buildbin-libdir && mkdir ChemmineOB.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ChemmineOB_1.22.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ChemmineOB.buildbin-libdir

StartedAt: 2019-10-16 08:18:59 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 08:20:28 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 89.5 seconds

RetCode: 0

Status:  OK

PackageFile: ChemmineOB_1.22.0.tgz

PackageFileSize: 3.462 MiB

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### Running command:
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###   rm -rf ChemmineOB.buildbin-libdir && mkdir ChemmineOB.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ChemmineOB_1.22.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ChemmineOB.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ChemmineOB.buildbin-libdir ChemmineOB_1.22.0.tar.gz'
>>>>>>> 

* installing *source* package ‘ChemmineOB’ ...
** using staged installation
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENBABEL... yes
checking for OPENBABEL... yes
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/Cellar/open-babel/2.4.1/include/openbabel-2.0    -I/usr/include/eigen3  -DUSE_BOOST -fPIC  -Wall -g -O2  -c ChemmineOB.cpp -o ChemmineOB.o
ChemmineOB.cpp:563:7: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
      register size_t l = 0;
      ^~~~~~~~~
ChemmineOB.cpp:564:7: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
      register size_t r = iter->size - 1;
      ^~~~~~~~~
ChemmineOB.cpp:567:2: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
        register size_t i = (l + r) >> 1; 
        ^~~~~~~~~
ChemmineOB.cpp:570:4: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
          register int compare = strcmp(name, iname);
          ^~~~~~~~~
ChemmineOB.cpp:614:7: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
      register size_t i = 0;
      ^~~~~~~~~
ChemmineOB.cpp:633:3: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
  register const unsigned char *u = (unsigned char *) ptr;
  ^~~~~~~~~
ChemmineOB.cpp:634:3: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
  register const unsigned char *eu =  u + sz;
  ^~~~~~~~~
ChemmineOB.cpp:636:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
    register unsigned char uu = *u;
    ^~~~~~~~~
ChemmineOB.cpp:648:3: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
  register unsigned char *u = (unsigned char *) ptr;
  ^~~~~~~~~
ChemmineOB.cpp:649:3: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
  register const unsigned char *eu = u + sz;
  ^~~~~~~~~
ChemmineOB.cpp:651:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
    register char d = *(c++);
    ^~~~~~~~~
ChemmineOB.cpp:652:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
    register unsigned char uu;
    ^~~~~~~~~
In file included from ChemmineOB.cpp:1476:
/usr/local/Cellar/open-babel/2.4.1/include/openbabel-2.0/openbabel/griddata.h:74:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual]
    double GetValue(int i, int j, int k) const;
           ^
/usr/local/Cellar/open-babel/2.4.1/include/openbabel-2.0/openbabel/base.h:229:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 3)
    virtual const std::string &GetValue()  const
                               ^
In file included from ChemmineOB.cpp:1476:
/usr/local/Cellar/open-babel/2.4.1/include/openbabel-2.0/openbabel/griddata.h:76:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual]
    double GetValue (vector3 pos) const;
           ^
/usr/local/Cellar/open-babel/2.4.1/include/openbabel-2.0/openbabel/base.h:229:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 1)
    virtual const std::string &GetValue()  const
                               ^
In file included from ChemmineOB.cpp:1493:
In file included from /usr/local/Cellar/open-babel/2.4.1/include/openbabel-2.0/openbabel/forcefield.h:32:
/usr/local/Cellar/open-babel/2.4.1/include/openbabel-2.0/openbabel/grid.h:123:10: warning: 'OpenBabel::OBFloatGrid::Init' hides overloaded virtual function [-Woverloaded-virtual]
    void Init(OBMol &box,double spacing, double pad=0.0);
         ^
/usr/local/Cellar/open-babel/2.4.1/include/openbabel-2.0/openbabel/grid.h:55:18: note: hidden overloaded virtual function 'OpenBabel::OBGrid::Init' declared here: different number of parameters (1 vs 3)
    virtual void Init(OBMol &box);
                 ^
ChemmineOB.cpp:31483:14: warning: explicitly assigning value of variable of type 'void *' to itself [-Wself-assign]
  clientdata = clientdata;
  ~~~~~~~~~~ ^ ~~~~~~~~~~
16 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/Cellar/open-babel/2.4.1/include/openbabel-2.0    -I/usr/include/eigen3  -DUSE_BOOST -fPIC  -Wall -g -O2  -c canonical.cpp -o canonical.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ChemmineOB.so ChemmineOB.o canonical.o -L/usr/local/Cellar/open-babel/2.4.1/lib -lopenbabel -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/ChemmineOB.buildbin-libdir/00LOCK-ChemmineOB/00new/ChemmineOB/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘copyToR’ with signature ‘"_p_std::pair<(unsigned int,unsigned int)>"’: no definition for class “_p_std::pair<(unsigned int,unsigned int)>”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::DoubleType"’: no definition for class “_p_OpenBabel::DoubleType”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::CharPtrLess"’: no definition for class “_p_OpenBabel::CharPtrLess”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::FptIndexHeader"’: no definition for class “_p_OpenBabel::FptIndexHeader”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::LineSearchType"’: no definition for class “_p_OpenBabel::LineSearchType”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ChemmineOB)


>>>>>>> 
>>>>>>> FIXING LINKS FOR ChemmineOB.buildbin-libdir/ChemmineOB/libs//ChemmineOB.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "ChemmineOB.buildbin-libdir/ChemmineOB/libs//ChemmineOB.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "ChemmineOB.buildbin-libdir/ChemmineOB/libs//ChemmineOB.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "ChemmineOB.buildbin-libdir/ChemmineOB/libs//ChemmineOB.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "ChemmineOB.buildbin-libdir/ChemmineOB/libs//ChemmineOB.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "ChemmineOB.buildbin-libdir/ChemmineOB/libs//ChemmineOB.so"