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BioC 3.0: BUILD BIN report for ChemmineOB on oaxaca

This page was generated on 2015-04-10 10:07:50 -0700 (Fri, 10 Apr 2015).

Package 143/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChemmineOB 1.4.1
Kevin Horan
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/ChemmineOB
Last Changed Rev: 99842 / Revision: 102249
Last Changed Date: 2015-02-25 23:00:40 -0800 (Wed, 25 Feb 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS [ OK ]

Summary

Package: ChemmineOB
Version: 1.4.1
Command: rm -rf ChemmineOB.buildbin-libdir && mkdir ChemmineOB.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ChemmineOB_1.4.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ChemmineOB.buildbin-libdir
StartedAt: 2015-04-10 04:28:30 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:29:31 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 61.4 seconds
RetCode: 0
Status:  OK 
PackageFile: ChemmineOB_1.4.1.tgz
PackageFileSize: 2.363 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf ChemmineOB.buildbin-libdir && mkdir ChemmineOB.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ChemmineOB_1.4.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ChemmineOB.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ChemmineOB.buildbin-libdir ChemmineOB_1.4.1.tar.gz'
>>>>>>> 

* installing *source* package ‘ChemmineOB’ ...
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++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -stdlib=libstdc++ -I/usr/local/include/openbabel-2.0    -I/usr/include/eigen3  -DUSE_BOOST -fPIC  -Wall -mtune=core2 -g -O2  -c ChemmineOB.cpp -o ChemmineOB.o
In file included from ChemmineOB.cpp:1476:
/usr/local/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/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/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/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/include/openbabel-2.0/openbabel/forcefield.h:32:
/usr/local/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/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 a variable of type 'void *' to itself [-Wself-assign]
  clientdata = clientdata;
  ˜˜˜˜˜˜˜˜˜˜ ^ ˜˜˜˜˜˜˜˜˜˜
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -stdlib=libstdc++ -I/usr/local/include/openbabel-2.0    -I/usr/include/eigen3  -DUSE_BOOST -fPIC  -Wall -mtune=core2 -g -O2  -c canonical.cpp -o canonical.o
clang++ -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 -stdlib=libstdc++ -L/usr/local/lib -lopenbabel -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/ChemmineOB.buildbin-libdir/ChemmineOB/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘ChemmineOB’
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
* 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/3.1/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/3.1/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/3.1/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/3.1/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/3.1/Resources/lib/libquadmath.0.dylib" "ChemmineOB.buildbin-libdir/ChemmineOB/libs//ChemmineOB.so"