BioC 3.0: BUILD BIN report for IRanges on oaxaca

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### Running command:
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###   rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh IRanges_2.0.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R IRanges.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=IRanges.buildbin-libdir IRanges_2.0.1.tar.gz'
>>>>>>> 

* installing *source* package ‘IRanges’ ...
** 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/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
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/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c CompressedList_class.c -o CompressedList_class.o
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/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c DataFrame_class.c -o DataFrame_class.o
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/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c GappedRanges_class.c -o GappedRanges_class.o
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/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Grouping_class.c -o Grouping_class.o
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/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c IRanges_class.c -o IRanges_class.o
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/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c IRanges_constructor.c -o IRanges_constructor.o
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/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c IntervalTree.c -o IntervalTree.o
IntervalTree.c:357:14: warning: variable 'result_inds' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  } else if (find_type == FIND_ARBITRARY) {
             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
IntervalTree.c:362:24: note: uninitialized use occurs here
  int *r_elt = INTEGER(result_inds);
                       ^˜˜˜˜˜˜˜˜˜˜
IntervalTree.c:357:10: note: remove the 'if' if its condition is always true
  } else if (find_type == FIND_ARBITRARY) {
         ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
IntervalTree.c:348:19: note: initialize the variable 'result_inds' to silence this warning
  SEXP result_inds;
                  ^
                   = NULL
IntervalTree.c:392:14: warning: variable 'result_inds' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  } else if (find_type == FIND_ARBITRARY) {
             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
IntervalTree.c:395:18: note: uninitialized use occurs here
  memset(INTEGER(result_inds), 0, LENGTH(result_inds) * sizeof(int));
                 ^˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:77:27: note: expanded from macro 'memset'
  __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))
                          ^
IntervalTree.c:392:10: note: remove the 'if' if its condition is always true
  } else if (find_type == FIND_ARBITRARY) {
         ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
IntervalTree.c:380:19: note: initialize the variable 'result_inds' to silence this warning
  SEXP result_inds;
                  ^
                   = NULL
2 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/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c NCList.c -o NCList.o
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/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_IRanges.c -o R_init_IRanges.o
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/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RangedData_class.c -o RangedData_class.o
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/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Ranges_class.c -o Ranges_class.o
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/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Ranges_comparison.c -o Ranges_comparison.o
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/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RleViews_utils.c -o RleViews_utils.o
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/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
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/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c SimpleRangesList_class.c -o SimpleRangesList_class.o
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/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c common.c -o common.o
common.c:13:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: common.c,v 1.117 2008/05/31 07:39:20 galt Exp $";
                  ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c coverage_methods.c -o coverage_methods.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c dlist.c -o dlist.o
dlist.c:8:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: dlist.c,v 1.11 2005/07/04 18:44:09 markd Exp $";
                  ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c errabort.c -o errabort.o
errabort.c:18:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: errabort.c,v 1.13 2004/11/10 00:10:50 markd Exp $";
                  ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c inter_range_methods.c -o inter_range_methods.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c localmem.c -o localmem.o
localmem.c:14:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: localmem.c,v 1.10 2005/04/11 07:20:03 markd Exp $";
                  ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c memalloc.c -o memalloc.o
memalloc.c:16:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: memalloc.c,v 1.31 2007/04/24 18:35:43 hiram Exp $";
                  ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c rbTree.c -o rbTree.o
rbTree.c:12:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: rbTree.c,v 1.11 2007/11/26 02:09:52 kent Exp $";
                  ^
1 warning 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/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc_handlers.c -o ucsc_handlers.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 IRanges.so CompressedIRangesList_class.o CompressedList_class.o DataFrame_class.o GappedRanges_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o IntervalTree.o NCList.o R_init_IRanges.o RangedData_class.o Ranges_class.o Ranges_comparison.o RleViews_utils.o S4Vectors_stubs.o SimpleRangesList_class.o common.o coverage_methods.o dlist.o errabort.o inter_range_methods.o localmem.o memalloc.o rbTree.o ucsc_handlers.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/IRanges.buildbin-libdir/IRanges/libs
** R
** inst
** preparing package for lazy loading
Warning: undefined slot classes in definition of "RangesNSBS": subscript(class "Ranges")
in method for ‘NSBS’ with signature ‘"Ranges"’: no definition for class “Ranges”
in method for ‘extractROWS’ with signature ‘"vectorORfactor","Ranges"’: no definition for class “Ranges”
in method for ‘extractROWS’ with signature ‘"matrix","Ranges"’: no definition for class “Ranges”
Creating a generic function for ‘head’ from package ‘utils’ in package ‘IRanges’
Creating a generic function for ‘tail’ from package ‘utils’ in package ‘IRanges’
Creating a generic function for ‘window’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘window<-’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘rev’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘with’ from package ‘base’ in package ‘IRanges’
in method for ‘coerce’ with signature ‘"Hits","IntegerList"’: no definition for class “IntegerList”
Creating a generic function for ‘stack’ from package ‘utils’ in package ‘IRanges’
in method for ‘!’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
in method for ‘match’ with signature ‘"CompressedList","list"’: no definition for class “CompressedList”
in method for ‘match’ with signature ‘"CompressedList","vector"’: no definition for class “CompressedList”
in method for ‘duplicated’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
in method for ‘unique’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
in method for ‘is.na’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
Creating a generic function for ‘mean’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘which.max’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘which.min’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘split’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘split<-’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘which’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘diff’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘var’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘cov’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘cor’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘sd’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘median’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘quantile’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘mad’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘IQR’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (IRanges)


>>>>>>> 
>>>>>>> FIXING LINKS FOR IRanges.buildbin-libdir/IRanges/libs//IRanges.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" "IRanges.buildbin-libdir/IRanges/libs//IRanges.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.3.dylib" "IRanges.buildbin-libdir/IRanges/libs//IRanges.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" "IRanges.buildbin-libdir/IRanges/libs//IRanges.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.dylib" "IRanges.buildbin-libdir/IRanges/libs//IRanges.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libquadmath.0.dylib" "IRanges.buildbin-libdir/IRanges/libs//IRanges.so"
BioC 3.0: BUILD BIN report for IRanges on oaxaca

Summary

Command output
