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BioC 2.14: BUILD BIN report for Biostrings on morelia

This page was generated on 2014-10-08 09:02:12 -0700 (Wed, 08 Oct 2014).

Package 98/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biostrings 2.32.1
H. Pages
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/Biostrings
Last Changed Rev: 92179 / Revision: 95116
Last Changed Date: 2014-07-03 18:14:24 -0700 (Thu, 03 Jul 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS [ OK ]

Summary

Package: Biostrings
Version: 2.32.1
Command: rm -rf Biostrings.buildbin-libdir && mkdir Biostrings.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Biostrings_2.32.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Biostrings.buildbin-libdir
StartedAt: 2014-10-08 02:47:48 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 02:48:09 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 20.7 seconds
RetCode: 0
Status:  OK 
PackageFile: Biostrings_2.32.1.tgz
PackageFileSize: 2.19 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Biostrings.buildbin-libdir && mkdir Biostrings.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Biostrings_2.32.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Biostrings.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Biostrings.buildbin-libdir Biostrings_2.32.1.tar.gz'
>>>>>>> 

* installing *source* package ‘Biostrings’ ...
** 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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c BAB_class.c -o BAB_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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c BitMatrix.c -o BitMatrix.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c IRanges_stubs.c -o IRanges_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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c MIndex_class.c -o MIndex_class.o
MIndex_class.c:192:18: warning: unused variable 'poffsets_order' [-Wunused-variable]
        IntAE poffsets, poffsets_order;
                        ^
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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c PreprocessedTB_class.c -o PreprocessedTB_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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_Biostrings.c -o R_init_Biostrings.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RoSeqs_utils.c -o RoSeqs_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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c SparseList_utils.c -o SparseList_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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c XStringSetList_class.c -o XStringSetList_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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c XStringSet_class.c -o XStringSet_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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c XStringSet_io.c -o XStringSet_io.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c XString_class.c -o XString_class.o
XString_class.c:174:6: warning: variable 'lkup_length' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
        if (lkup == R_NilValue) {
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
XString_class.c:181:30: note: uninitialized use occurs here
                        INTEGER(start)[0], lkup0, lkup_length);
                                                  ^˜˜˜˜˜˜˜˜˜˜
XString_class.c:174:2: note: remove the 'if' if its condition is always false
        if (lkup == R_NilValue) {
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
XString_class.c:164:17: note: initialize the variable 'lkup_length' to silence this warning
        int lkup_length;
                       ^
                        = 0
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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c XVector_stubs.c -o XVector_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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c align_needwunsQS.c -o align_needwunsQS.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c align_pairwiseAlignment.c -o align_pairwiseAlignment.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c align_utils.c -o align_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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c find_palindromes.c -o find_palindromes.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c gtestsim.c -o gtestsim.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c inject_code.c -o inject_code.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c io_utils.c -o io_utils.o
io_utils.c:373:43: warning: variable 'subtype' is uninitialized when used here [-Wuninitialized]
                file = oZFile_open(expath, mode, ztype, subtype);
                                                        ^˜˜˜˜˜˜
io_utils.c:363:20: note: initialize the variable 'subtype' to silence this warning
        int ztype, subtype;
                          ^
                           = 0
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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c letter_frequency.c -o letter_frequency.o
letter_frequency.c:956:13: warning: unused variable 'ans_dimnames' [-Wunused-variable]
  SEXP ans, ans_dimnames;
            ^
letter_frequency.c:957:48: warning: unused variable 'x_pos' [-Wunused-variable]
  int x_width, y_width, x_length, *ans_mat, i, x_pos;
                                               ^
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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c lowlevel_matching.c -o lowlevel_matching.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_BOC.c -o match_BOC.o
match_BOC.c:268:55: warning: unused variable 'j' [-Wunused-variable]
            nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                             ^
match_BOC.c:268:59: warning: unused variable 'offsets' [-Wunused-variable]
            nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                                 ^
match_BOC.c:268:68: warning: unused variable 'noffsets' [-Wunused-variable]
            nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                                          ^
match_BOC.c:331:3: warning: unused label 'continue0' [-Wunused-label]
                continue0: ;
                ^˜˜˜˜˜˜˜˜˜˜
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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_BOC2.c -o match_BOC2.o
match_BOC2.c:234:55: warning: unused variable 'j' [-Wunused-variable]
            nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                             ^
match_BOC2.c:234:59: warning: unused variable 'offsets' [-Wunused-variable]
            nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                                 ^
match_BOC2.c:234:68: warning: unused variable 'noffsets' [-Wunused-variable]
            nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                                          ^
match_BOC2.c:288:3: warning: unused label 'continue0' [-Wunused-label]
                continue0: ;
                ^˜˜˜˜˜˜˜˜˜˜
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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_PWM.c -o match_PWM.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_pattern.c -o match_pattern.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_pattern_boyermoore.c -o match_pattern_boyermoore.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_pattern_indels.c -o match_pattern_indels.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_pattern_shiftor.c -o match_pattern_shiftor.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_pdict.c -o match_pdict.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c:640:21: warning: unused function 'a_nice_max_nodeextbuf_nelt' [-Wunused-function]
static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
                    ^
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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_pdict_Twobit.c -o match_pdict_Twobit.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c:665:49: warning: unused variable 'ncol' [-Wunused-variable]
        int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
                                                       ^
match_pdict_utils.c:723:6: warning: unused variable 'nelt' [-Wunused-variable]
        int nelt, nkey0, nkey1, nkey2, i;
            ^
match_pdict_utils.c:822:33: warning: unused variable 'NFC' [-Wunused-variable]
        unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                                       ^
match_pdict_utils.c:822:26: warning: unused variable 'nloci' [-Wunused-variable]
        unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                                ^
match_pdict_utils.c:822:20: warning: unused variable 'ndup' [-Wunused-variable]
        unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                          ^
match_pdict_utils.c:823:44: warning: unused variable 'subtotal_NFC' [-Wunused-variable]
        static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                                                  ^
match_pdict_utils.c:823:27: warning: unused variable 'total_NFC' [-Wunused-variable]
        static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                                 ^
match_pdict_utils.c:275:13: warning: unused function 'match_headtail_by_loc' [-Wunused-function]
static void match_headtail_by_loc(const HeadTail *headtail,
            ^
8 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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_reporting.c -o match_reporting.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c matchprobes.c -o matchprobes.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pmatchPattern.c -o pmatchPattern.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c replace_letter_at.c -o replace_letter_at.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c strutils.c -o strutils.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c translate.c -o translate.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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c unstrsplit_methods.c -o unstrsplit_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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c utils.c -o 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/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c xscat.c -o xscat.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XStringSet_io.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o io_utils.o letter_frequency.o lowlevel_matching.o match_BOC.o match_BOC2.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/Biostrings.buildbin-libdir/Biostrings/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘setequal’ from package ‘base’ in package ‘Biostrings’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’
Creating a new generic function for ‘offset’ in package ‘Biostrings’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Biostrings)


>>>>>>> 
>>>>>>> FIXING LINKS FOR Biostrings.buildbin-libdir/Biostrings/libs//Biostrings.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" "Biostrings.buildbin-libdir/Biostrings/libs//Biostrings.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.3.dylib" "Biostrings.buildbin-libdir/Biostrings/libs//Biostrings.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" "Biostrings.buildbin-libdir/Biostrings/libs//Biostrings.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.dylib" "Biostrings.buildbin-libdir/Biostrings/libs//Biostrings.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libquadmath.0.dylib" "Biostrings.buildbin-libdir/Biostrings/libs//Biostrings.so"