Package: runibic

Version: 1.6.0

Command: rm -rf runibic.buildbin-libdir && mkdir runibic.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh runibic_1.6.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R runibic.buildbin-libdir

StartedAt: 2019-10-16 09:20:48 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 09:22:04 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 75.8 seconds

RetCode: 0

Status:  OK

PackageFile: runibic_1.6.0.tgz

PackageFileSize: 134.1 KiB

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### Running command:
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###   rm -rf runibic.buildbin-libdir && mkdir runibic.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh runibic_1.6.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R runibic.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=runibic.buildbin-libdir runibic_1.6.0.tar.gz'
>>>>>>> 

* installing *source* package ‘runibic’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC  -Wall -g -O2  -c GlobalDefs.cpp -o GlobalDefs.o
GlobalDefs.cpp:117:7: warning: unused variable 'colNum' [-Wunused-variable]
  int colNum = gParameters.ColNumber;
      ^
GlobalDefs.cpp:280:37: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
    for (auto i=maxRecord.size()-1;i>=0;i--) {
                                   ~^ ~
GlobalDefs.cpp:232:16: warning: unused variable 'rank' [-Wunused-variable]
  int maxvalue,rank;
               ^
In file included from GlobalDefs.cpp:34:
./fibpriv.h:54:13: warning: unused function 'fh_initheap' [-Wunused-function]
static void fh_initheap(struct fibheap *);
            ^
./fibpriv.h:55:13: warning: unused function 'fh_insertrootlist' [-Wunused-function]
static void fh_insertrootlist(struct fibheap *, struct fibheap_el *);
            ^
./fibpriv.h:56:13: warning: unused function 'fh_removerootlist' [-Wunused-function]
static void fh_removerootlist(struct fibheap *, struct fibheap_el *);
            ^
./fibpriv.h:57:13: warning: unused function 'fh_consolidate' [-Wunused-function]
static void fh_consolidate(struct fibheap *);
            ^
./fibpriv.h:58:13: warning: unused function 'fh_heaplink' [-Wunused-function]
static void fh_heaplink(struct fibheap *h, struct fibheap_el *y,
            ^
./fibpriv.h:60:13: warning: unused function 'fh_cut' [-Wunused-function]
static void fh_cut(struct fibheap *, struct fibheap_el *, struct fibheap_el *);
            ^
./fibpriv.h:61:13: warning: unused function 'fh_cascading_cut' [-Wunused-function]
static void fh_cascading_cut(struct fibheap *, struct fibheap_el *);
            ^
./fibpriv.h:62:27: warning: unused function 'fh_extractminel' [-Wunused-function]
static struct fibheap_el *fh_extractminel(struct fibheap *);
                          ^
./fibpriv.h:63:13: warning: unused function 'fh_checkcons' [-Wunused-function]
static void fh_checkcons(struct fibheap *h);
            ^
./fibpriv.h:64:13: warning: unused function 'fh_destroyheap' [-Wunused-function]
static void fh_destroyheap(struct fibheap *h);
            ^
./fibpriv.h:65:12: warning: unused function 'fh_compare' [-Wunused-function]
static int fh_compare(struct fibheap *h, struct fibheap_el *a,
           ^
./fibpriv.h:67:12: warning: unused function 'fh_comparedata' [-Wunused-function]
static int fh_comparedata(struct fibheap *h, int key, void *data,
           ^
./fibpriv.h:69:13: warning: unused function 'fh_insertel' [-Wunused-function]
static void fh_insertel(struct fibheap *h, struct fibheap_el *x);
            ^
./fibpriv.h:70:13: warning: unused function 'fh_deleteel' [-Wunused-function]
static void fh_deleteel(struct fibheap *h, struct fibheap_el *x);
            ^
./fibpriv.h:86:27: warning: unused function 'fhe_newelem' [-Wunused-function]
static struct fibheap_el *fhe_newelem(void);
                          ^
./fibpriv.h:87:13: warning: unused function 'fhe_initelem' [-Wunused-function]
static void fhe_initelem(struct fibheap_el *);
            ^
./fibpriv.h:88:13: warning: unused function 'fhe_insertafter' [-Wunused-function]
static void fhe_insertafter(struct fibheap_el *a, struct fibheap_el *b);
            ^
./fibpriv.h:90:27: warning: unused function 'fhe_remove' [-Wunused-function]
static struct fibheap_el *fhe_remove(struct fibheap_el *a);
                          ^
21 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c fib.c -o fib.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC  -Wall -g -O2  -c runibic.cpp -o runibic.o
runibic.cpp:567:13: warning: unused variable 'temp' [-Wunused-variable]
        int temp;
            ^
1 warning generated.
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 runibic.so GlobalDefs.o RcppExports.o fib.o runibic.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/runibic.buildbin-libdir/00LOCK-runibic/00new/runibic/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (runibic)


>>>>>>> 
>>>>>>> FIXING LINKS FOR runibic.buildbin-libdir/runibic/libs//runibic.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" "runibic.buildbin-libdir/runibic/libs//runibic.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "runibic.buildbin-libdir/runibic/libs//runibic.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" "runibic.buildbin-libdir/runibic/libs//runibic.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "runibic.buildbin-libdir/runibic/libs//runibic.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "runibic.buildbin-libdir/runibic/libs//runibic.so"