Package: Biostrings

Version: 2.22.0

Command: rm -rf Biostrings.buildbin-libdir && mkdir Biostrings.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Biostrings_2.22.0.tar.gz /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R Biostrings.buildbin-libdir

StartedAt: 2012-03-24 05:07:35 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 05:08:38 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 62.9 seconds

RetCode: 0

Status:  OK

PackageFile: Biostrings_2.22.0.tgz

PackageFileSize: 2.227 MiB

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Biostrings.buildbin-libdir Biostrings_2.22.0.tar.gz'
>>>>>>> 

* installing *source* package 'Biostrings' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c BAB_class.c -o BAB_class.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c BitMatrix.c -o BitMatrix.o
BitMatrix.c: In function 'debug_BitMatrix':
BitMatrix.c:382: warning: left shift count >= width of type
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function 'SparseMIndex_endIndex':
MIndex_class.c:192: warning: unused variable 'poffsets_order'
MIndex_class.c: In function '_get_cachedMIndex_elt':
MIndex_class.c:93: warning: 'cached_iranges.end' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c SparseList_utils.c -o SparseList_utils.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function 'new_XStringSet_from_CHARACTER':
XStringSet_class.c:92: warning: 'lkup_length' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c XStringSet_io.c -o XStringSet_io.o
XStringSet_io.c: In function 'parse_FASTQ_file':
XStringSet_io.c:546: warning: 'load_record' may be used uninitialized in this function
XStringSet_io.c: In function 'read_fastq_in_XStringSet':
XStringSet_io.c:510: warning: 'loader_ext.lkup_length' may be used uninitialized in this function
XStringSet_io.c:510: note: 'loader_ext.lkup_length' was declared here
XStringSet_io.c: In function 'read_fasta_in_XStringSet':
XStringSet_io.c:319: warning: 'loader_ext.cached_ans_elt.length' is used uninitialized in this function
XStringSet_io.c:319: warning: 'loader_ext.cached_ans_elt.seq' is used uninitialized in this function
XStringSet_io.c:166: warning: 'loader_ext.lkup_length' may be used uninitialized in this function
XStringSet_io.c:166: note: 'loader_ext.lkup_length' was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c XString_class.c -o XString_class.o
XString_class.c: In function 'new_XString_from_CHARACTER':
XString_class.c:162: warning: 'lkup_length' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function 'align_needwunsQS':
align_needwunsQS.c:39: warning: 'lkup_val' may be used uninitialized in this function
align_needwunsQS.c:39: note: 'lkup_val' was declared here
align_needwunsQS.c:26: warning: 'sc' may be used uninitialized in this function
align_needwunsQS.c:26: note: 'sc' was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c align_utils.c -o align_utils.o
align_utils.c: In function 'PairwiseAlignedFixedSubject_align_aligned':
align_utils.c:223: warning: 'indelWidthSubject' may be used uninitialized in this function
align_utils.c:223: warning: 'indelStartSubject' may be used uninitialized in this function
align_utils.c:223: warning: 'indelWidthPattern' may be used uninitialized in this function
align_utils.c:223: warning: 'indelStartPattern' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c find_palindromes.c -o find_palindromes.o
find_palindromes.c: In function 'find_palindromes':
find_palindromes.c:26: warning: 'letter0' may be used uninitialized in this function
find_palindromes.c:26: note: 'letter0' was declared here
find_palindromes.c:25: warning: 'all_letter0' may be used uninitialized in this function
find_palindromes.c:25: note: 'all_letter0' was declared here
find_palindromes.c:82: warning: 'letter0' may be used uninitialized in this function
find_palindromes.c:82: note: 'letter0' was declared here
find_palindromes.c:81: warning: 'lkup_val' may be used uninitialized in this function
find_palindromes.c:81: note: 'lkup_val' was declared here
find_palindromes.c:81: warning: 'all_letter0' may be used uninitialized in this function
find_palindromes.c:81: note: 'all_letter0' was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c gtestsim.c -o gtestsim.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c inject_code.c -o inject_code.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c io_utils.c -o io_utils.o
io_utils.c: In function 'open_input_file':
io_utils.c:70: warning: unused variable 'buf'
io_utils.c:69: warning: unused variable 'ret'
io_utils.c: In function 'new_input_ExternalFilePtr':
io_utils.c:68: warning: 'fp' may be used uninitialized in this function
io_utils.c:68: note: 'fp' was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c letter_frequency.c -o letter_frequency.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c lowlevel_matching.c -o lowlevel_matching.o
lowlevel_matching.c: In function 'XStringSet_vmatch_pattern_at':
lowlevel_matching.c:584: warning: 'ans_nrow' may be used uninitialized in this function
lowlevel_matching.c:584: warning: 'ans_elt' may be used uninitialized in this function
lowlevel_matching.c:586: warning: 'ans' may be used uninitialized in this function
lowlevel_matching.c: In function 'XString_match_pattern_at':
lowlevel_matching.c:536: warning: 'ans' may be used uninitialized in this function
lowlevel_matching.c:534: warning: 'ans_elt' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_BOC.c -o match_BOC.o
match_BOC.c: In function 'BOC_preprocess':
match_BOC.c:82: warning: overflow in implicit constant conversion
match_BOC.c: In function 'BOC_exact_search':
match_BOC.c:331: warning: label 'continue0' defined but not used
match_BOC.c:268: warning: unused variable 'noffsets'
match_BOC.c:268: warning: unused variable 'offsets'
match_BOC.c:268: warning: unused variable 'j'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_BOC2.c -o match_BOC2.o
match_BOC2.c: In function 'BOC2_exact_search':
match_BOC2.c:288: warning: label 'continue0' defined but not used
match_BOC2.c:234: warning: unused variable 'noffsets'
match_BOC2.c:234: warning: unused variable 'offsets'
match_BOC2.c:234: warning: unused variable 'j'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_PWM.c -o match_PWM.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_WCP.c -o match_WCP.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pattern.c -o match_pattern.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
match_pattern_boyermoore.c: In function '_match_pattern_boyermoore':
match_pattern_boyermoore.c:401: warning: 'c' may be used uninitialized in this function
match_pattern_boyermoore.c:399: warning: 'j1' may be used uninitialized in this function
match_pattern_boyermoore.c:399: warning: 'i2' may be used uninitialized in this function
match_pattern_boyermoore.c:399: warning: 'i1' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pattern_indels.c -o match_pattern_indels.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pdict.c -o match_pdict.o
match_pdict.c: In function 'init_vcount_collapsed_ans':
match_pdict.c:110: warning: 'ans_length' may be used uninitialized in this function
match_pdict.c: In function 'vmatch_XStringSet_XStringSet':
match_pdict.c:463: warning: 'ans_elt' may be used uninitialized in this function
match_pdict.c:463: note: 'ans_elt' was declared here
match_pdict.c: In function 'vmatch_PDict3Parts_XStringSet':
match_pdict.c:414: warning: 'ans_col' may be used uninitialized in this function
match_pdict.c:414: note: 'ans_col' was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c:641: warning: 'a_nice_max_nodeextbuf_nelt' defined but not used
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pdict_Twobit.c -o match_pdict_Twobit.o
match_pdict_Twobit.c: In function 'build_Twobit':
match_pdict_Twobit.c:125: warning: 'twobit_sign2pos' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function 'match_ppheadtail0':
match_pdict_utils.c:664: warning: unused variable 'ncol'
match_pdict_utils.c: In function 'match_ppheadtail':
match_pdict_utils.c:722: warning: unused variable 'nelt'
match_pdict_utils.c: In function '_match_pdict_all_flanks':
match_pdict_utils.c:821: warning: unused variable 'subtotal_NFC'
match_pdict_utils.c:821: warning: unused variable 'total_NFC'
match_pdict_utils.c:820: warning: unused variable 'NFC'
match_pdict_utils.c:820: warning: unused variable 'nloci'
match_pdict_utils.c:820: warning: unused variable 'ndup'
match_pdict_utils.c: At top level:
match_pdict_utils.c:279: warning: 'match_headtail_by_loc' defined but not used
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_reporting.c -o match_reporting.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c matchprobes.c -o matchprobes.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c pmatchPattern.c -o pmatchPattern.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c replace_letter_at.c -o replace_letter_at.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c strutils.c -o strutils.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c translate.c -o translate.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c utils.c -o utils.o
utils.c: In function '_get_twobit_signature_at':
utils.c:210: warning: 'twobit_sign' may be used uninitialized in this function
utils.c: In function '_get_twobit_signature':
utils.c:196: warning: 'twobit_sign' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c xscat.c -o xscat.o
xscat.c: In function 'XStringSet_xscat':
xscat.c:94: warning: 'ans_length' is used uninitialized in this function
xscat.c:70: warning: 'ans_element_type' may be used uninitialized in this function
xscat.c: In function 'XString_xscat':
xscat.c:36: warning: 'ans_length' is used uninitialized in this function
xscat.c:18: warning: 'ans_classname' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -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 XStringSet_class.o XStringSet_io.o XString_class.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_WCP.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 utils.o xscat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/Biostrings.buildbin-libdir/Biostrings/libs/i386
** 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 ...
*** tangling vignette sources ...
   'Alignments.Rnw' 
   'Biostrings2Classes.Rnw' 
   'MultipleAlignments.Rnw' 
   'matchprobes.Rnw' 
** testing if installed package can be loaded

* DONE (Biostrings)


>>>>>>> 
>>>>>>> FIXING LINKS FOR Biostrings.buildbin-libdir/Biostrings/libs/i386/Biostrings.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgcc_s.1.dylib" "Biostrings.buildbin-libdir/Biostrings/libs/i386/Biostrings.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "Biostrings.buildbin-libdir/Biostrings/libs/i386/Biostrings.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.5.2.dylib" "Biostrings.buildbin-libdir/Biostrings/libs/i386/Biostrings.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "Biostrings.buildbin-libdir/Biostrings/libs/i386/Biostrings.so"


>>>>>>> 
>>>>>>> INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --no-multiarch --no-test-load --library=Biostrings.buildbin-libdir --libs-only Biostrings_2.22.0.tar.gz'
>>>>>>> 

* installing *source* package 'Biostrings' ...
** libs
*** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c BAB_class.c -o BAB_class.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c BitMatrix.c -o BitMatrix.o
BitMatrix.c: In function 'debug_BitMatrix':
BitMatrix.c:382: warning: left shift count >= width of type
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function 'SparseMIndex_endIndex':
MIndex_class.c:192: warning: unused variable 'poffsets_order'
MIndex_class.c: In function '_get_cachedMIndex_elt':
MIndex_class.c:93: warning: 'cached_iranges.end' may be used uninitialized in this function
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c SparseList_utils.c -o SparseList_utils.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function 'new_XStringSet_from_CHARACTER':
XStringSet_class.c:92: warning: 'lkup_length' may be used uninitialized in this function
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c XStringSet_io.c -o XStringSet_io.o
XStringSet_io.c: In function 'parse_FASTQ_file':
XStringSet_io.c:546: warning: 'load_record' may be used uninitialized in this function
XStringSet_io.c: In function 'read_fastq_in_XStringSet':
XStringSet_io.c:510: warning: 'loader_ext.lkup_length' may be used uninitialized in this function
XStringSet_io.c:510: note: 'loader_ext.lkup_length' was declared here
XStringSet_io.c: In function 'read_fasta_in_XStringSet':
XStringSet_io.c:166: warning: 'loader_ext.lkup_length' may be used uninitialized in this function
XStringSet_io.c:166: note: 'loader_ext.lkup_length' was declared here
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c XString_class.c -o XString_class.o
XString_class.c: In function 'new_XString_from_CHARACTER':
XString_class.c:162: warning: 'lkup_length' may be used uninitialized in this function
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function 'align_needwunsQS':
align_needwunsQS.c:39: warning: 'lkup_val' may be used uninitialized in this function
align_needwunsQS.c:39: note: 'lkup_val' was declared here
align_needwunsQS.c:26: warning: 'sc' may be used uninitialized in this function
align_needwunsQS.c:26: note: 'sc' was declared here
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c align_utils.c -o align_utils.o
align_utils.c: In function 'PairwiseAlignedFixedSubject_align_aligned':
align_utils.c:223: warning: 'indelWidthSubject' may be used uninitialized in this function
align_utils.c:223: warning: 'indelStartSubject' may be used uninitialized in this function
align_utils.c:223: warning: 'indelWidthPattern' may be used uninitialized in this function
align_utils.c:223: warning: 'indelStartPattern' may be used uninitialized in this function
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c find_palindromes.c -o find_palindromes.o
find_palindromes.c: In function 'find_palindromes':
find_palindromes.c:26: warning: 'letter0' may be used uninitialized in this function
find_palindromes.c:26: note: 'letter0' was declared here
find_palindromes.c:25: warning: 'all_letter0' may be used uninitialized in this function
find_palindromes.c:25: note: 'all_letter0' was declared here
find_palindromes.c:82: warning: 'letter0' may be used uninitialized in this function
find_palindromes.c:82: note: 'letter0' was declared here
find_palindromes.c:81: warning: 'lkup_val' may be used uninitialized in this function
find_palindromes.c:81: note: 'lkup_val' was declared here
find_palindromes.c:81: warning: 'all_letter0' may be used uninitialized in this function
find_palindromes.c:81: note: 'all_letter0' was declared here
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c gtestsim.c -o gtestsim.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c inject_code.c -o inject_code.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c io_utils.c -o io_utils.o
io_utils.c: In function 'open_input_file':
io_utils.c:70: warning: unused variable 'buf'
io_utils.c:69: warning: unused variable 'ret'
io_utils.c: In function 'new_input_ExternalFilePtr':
io_utils.c:68: warning: 'fp' may be used uninitialized in this function
io_utils.c:68: note: 'fp' was declared here
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c letter_frequency.c -o letter_frequency.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c lowlevel_matching.c -o lowlevel_matching.o
lowlevel_matching.c: In function 'XStringSet_vmatch_pattern_at':
lowlevel_matching.c:586: warning: 'ans' may be used uninitialized in this function
lowlevel_matching.c:584: warning: 'ans_nrow' may be used uninitialized in this function
lowlevel_matching.c:584: warning: 'ans_elt' may be used uninitialized in this function
lowlevel_matching.c: In function 'XString_match_pattern_at':
lowlevel_matching.c:536: warning: 'ans' may be used uninitialized in this function
lowlevel_matching.c:534: warning: 'ans_elt' may be used uninitialized in this function
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_BOC.c -o match_BOC.o
match_BOC.c: In function 'BOC_preprocess':
match_BOC.c:82: warning: overflow in implicit constant conversion
match_BOC.c: In function 'BOC_exact_search':
match_BOC.c:331: warning: label 'continue0' defined but not used
match_BOC.c:268: warning: unused variable 'noffsets'
match_BOC.c:268: warning: unused variable 'offsets'
match_BOC.c:268: warning: unused variable 'j'
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_BOC2.c -o match_BOC2.o
match_BOC2.c: In function 'BOC2_exact_search':
match_BOC2.c:288: warning: label 'continue0' defined but not used
match_BOC2.c:234: warning: unused variable 'noffsets'
match_BOC2.c:234: warning: unused variable 'offsets'
match_BOC2.c:234: warning: unused variable 'j'
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_PWM.c -o match_PWM.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_WCP.c -o match_WCP.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pattern.c -o match_pattern.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
match_pattern_boyermoore.c: In function '_match_pattern_boyermoore':
match_pattern_boyermoore.c:401: warning: 'c' may be used uninitialized in this function
match_pattern_boyermoore.c:399: warning: 'j1' may be used uninitialized in this function
match_pattern_boyermoore.c:399: warning: 'i2' may be used uninitialized in this function
match_pattern_boyermoore.c:399: warning: 'i1' may be used uninitialized in this function
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pattern_indels.c -o match_pattern_indels.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pdict.c -o match_pdict.o
match_pdict.c: In function 'init_vcount_collapsed_ans':
match_pdict.c:110: warning: 'ans_length' may be used uninitialized in this function
match_pdict.c: In function 'vmatch_XStringSet_XStringSet':
match_pdict.c:463: warning: 'ans_elt' may be used uninitialized in this function
match_pdict.c:463: note: 'ans_elt' was declared here
match_pdict.c: In function 'vmatch_PDict3Parts_XStringSet':
match_pdict.c:414: warning: 'ans_col' may be used uninitialized in this function
match_pdict.c:414: note: 'ans_col' was declared here
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c:641: warning: 'a_nice_max_nodeextbuf_nelt' defined but not used
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pdict_Twobit.c -o match_pdict_Twobit.o
match_pdict_Twobit.c: In function 'build_Twobit':
match_pdict_Twobit.c:125: warning: 'twobit_sign2pos' may be used uninitialized in this function
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function 'match_ppheadtail0':
match_pdict_utils.c:664: warning: unused variable 'ncol'
match_pdict_utils.c: In function 'match_ppheadtail':
match_pdict_utils.c:722: warning: unused variable 'nelt'
match_pdict_utils.c: In function '_match_pdict_all_flanks':
match_pdict_utils.c:821: warning: unused variable 'subtotal_NFC'
match_pdict_utils.c:821: warning: unused variable 'total_NFC'
match_pdict_utils.c:820: warning: unused variable 'NFC'
match_pdict_utils.c:820: warning: unused variable 'nloci'
match_pdict_utils.c:820: warning: unused variable 'ndup'
match_pdict_utils.c: At top level:
match_pdict_utils.c:279: warning: 'match_headtail_by_loc' defined but not used
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_reporting.c -o match_reporting.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c matchprobes.c -o matchprobes.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c pmatchPattern.c -o pmatchPattern.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c replace_letter_at.c -o replace_letter_at.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c strutils.c -o strutils.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c translate.c -o translate.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c utils.c -o utils.o
utils.c: In function '_get_twobit_signature_at':
utils.c:210: warning: 'twobit_sign' may be used uninitialized in this function
utils.c: In function '_get_twobit_signature':
utils.c:196: warning: 'twobit_sign' may be used uninitialized in this function
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c xscat.c -o xscat.o
xscat.c: In function 'XStringSet_xscat':
xscat.c:94: warning: 'ans_length' is used uninitialized in this function
xscat.c:70: warning: 'ans_element_type' may be used uninitialized in this function
xscat.c: In function 'XString_xscat':
xscat.c:36: warning: 'ans_length' is used uninitialized in this function
xscat.c:18: warning: 'ans_classname' may be used uninitialized in this function
gcc -arch ppc -std=gnu99 -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 XStringSet_class.o XStringSet_io.o XString_class.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_WCP.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 utils.o xscat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/Biostrings.buildbin-libdir/Biostrings/libs/ppc

* DONE (Biostrings)


>>>>>>> 
>>>>>>> FIXING LINKS FOR Biostrings.buildbin-libdir/Biostrings/libs/ppc/Biostrings.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgcc_s.1.dylib" "Biostrings.buildbin-libdir/Biostrings/libs/ppc/Biostrings.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "Biostrings.buildbin-libdir/Biostrings/libs/ppc/Biostrings.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.5.2.dylib" "Biostrings.buildbin-libdir/Biostrings/libs/ppc/Biostrings.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "Biostrings.buildbin-libdir/Biostrings/libs/ppc/Biostrings.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=Biostrings.buildbin-libdir --libs-only Biostrings_2.22.0.tar.gz'
>>>>>>> 

* installing *source* package 'Biostrings' ...
** libs
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c BAB_class.c -o BAB_class.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c BitMatrix.c -o BitMatrix.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function 'SparseMIndex_endIndex':
MIndex_class.c:192: warning: unused variable 'poffsets_order'
MIndex_class.c: In function '_get_cachedMIndex_elt':
MIndex_class.c:93: warning: 'cached_iranges.end' may be used uninitialized in this function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c SparseList_utils.c -o SparseList_utils.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function 'new_XStringSet_from_CHARACTER':
XStringSet_class.c:92: warning: 'lkup_length' may be used uninitialized in this function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c XStringSet_io.c -o XStringSet_io.o
XStringSet_io.c: In function 'parse_FASTQ_file':
XStringSet_io.c:546: warning: 'load_record' may be used uninitialized in this function
XStringSet_io.c: In function 'read_fastq_in_XStringSet':
XStringSet_io.c:510: warning: 'loader_ext.lkup_length' may be used uninitialized in this function
XStringSet_io.c:510: note: 'loader_ext.lkup_length' was declared here
XStringSet_io.c: In function 'read_fasta_in_XStringSet':
XStringSet_io.c:319: warning: 'loader_ext.cached_ans_elt.length' is used uninitialized in this function
XStringSet_io.c:319: warning: 'loader_ext.cached_ans_elt.seq' is used uninitialized in this function
XStringSet_io.c:166: warning: 'loader_ext.lkup_length' may be used uninitialized in this function
XStringSet_io.c:166: note: 'loader_ext.lkup_length' was declared here
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c XString_class.c -o XString_class.o
XString_class.c: In function 'new_XString_from_CHARACTER':
XString_class.c:162: warning: 'lkup_length' may be used uninitialized in this function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function 'align_needwunsQS':
align_needwunsQS.c:39: warning: 'lkup_val' may be used uninitialized in this function
align_needwunsQS.c:39: note: 'lkup_val' was declared here
align_needwunsQS.c:26: warning: 'sc' may be used uninitialized in this function
align_needwunsQS.c:26: note: 'sc' was declared here
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c align_utils.c -o align_utils.o
align_utils.c: In function 'PairwiseAlignedFixedSubject_align_aligned':
align_utils.c:223: warning: 'indelWidthSubject' may be used uninitialized in this function
align_utils.c:223: warning: 'indelStartSubject' may be used uninitialized in this function
align_utils.c:223: warning: 'indelWidthPattern' may be used uninitialized in this function
align_utils.c:223: warning: 'indelStartPattern' may be used uninitialized in this function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c find_palindromes.c -o find_palindromes.o
find_palindromes.c: In function 'find_palindromes':
find_palindromes.c:26: warning: 'letter0' may be used uninitialized in this function
find_palindromes.c:26: note: 'letter0' was declared here
find_palindromes.c:25: warning: 'all_letter0' may be used uninitialized in this function
find_palindromes.c:25: note: 'all_letter0' was declared here
find_palindromes.c:82: warning: 'letter0' may be used uninitialized in this function
find_palindromes.c:82: note: 'letter0' was declared here
find_palindromes.c:81: warning: 'lkup_val' may be used uninitialized in this function
find_palindromes.c:81: note: 'lkup_val' was declared here
find_palindromes.c:81: warning: 'all_letter0' may be used uninitialized in this function
find_palindromes.c:81: note: 'all_letter0' was declared here
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c gtestsim.c -o gtestsim.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c inject_code.c -o inject_code.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c io_utils.c -o io_utils.o
io_utils.c: In function 'open_input_file':
io_utils.c:70: warning: unused variable 'buf'
io_utils.c:69: warning: unused variable 'ret'
io_utils.c: In function 'new_input_ExternalFilePtr':
io_utils.c:68: warning: 'fp' may be used uninitialized in this function
io_utils.c:68: note: 'fp' was declared here
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c letter_frequency.c -o letter_frequency.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c lowlevel_matching.c -o lowlevel_matching.o
lowlevel_matching.c: In function 'XStringSet_vmatch_pattern_at':
lowlevel_matching.c:586: warning: 'ans' may be used uninitialized in this function
lowlevel_matching.c:584: warning: 'ans_nrow' may be used uninitialized in this function
lowlevel_matching.c:584: warning: 'ans_elt' may be used uninitialized in this function
lowlevel_matching.c: In function 'XString_match_pattern_at':
lowlevel_matching.c:536: warning: 'ans' may be used uninitialized in this function
lowlevel_matching.c:534: warning: 'ans_elt' may be used uninitialized in this function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_BOC.c -o match_BOC.o
match_BOC.c: In function 'BOC_preprocess':
match_BOC.c:82: warning: overflow in implicit constant conversion
match_BOC.c: In function 'BOC_exact_search':
match_BOC.c:331: warning: label 'continue0' defined but not used
match_BOC.c:268: warning: unused variable 'noffsets'
match_BOC.c:268: warning: unused variable 'offsets'
match_BOC.c:268: warning: unused variable 'j'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_BOC2.c -o match_BOC2.o
match_BOC2.c: In function 'BOC2_exact_search':
match_BOC2.c:288: warning: label 'continue0' defined but not used
match_BOC2.c:234: warning: unused variable 'noffsets'
match_BOC2.c:234: warning: unused variable 'offsets'
match_BOC2.c:234: warning: unused variable 'j'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_PWM.c -o match_PWM.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_WCP.c -o match_WCP.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pattern.c -o match_pattern.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
match_pattern_boyermoore.c: In function '_match_pattern_boyermoore':
match_pattern_boyermoore.c:399: warning: 'i1' may be used uninitialized in this function
match_pattern_boyermoore.c:401: warning: 'c' may be used uninitialized in this function
match_pattern_boyermoore.c:399: warning: 'j1' may be used uninitialized in this function
match_pattern_boyermoore.c:399: warning: 'i2' may be used uninitialized in this function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pattern_indels.c -o match_pattern_indels.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pdict.c -o match_pdict.o
match_pdict.c: In function 'init_vcount_collapsed_ans':
match_pdict.c:110: warning: 'ans_length' may be used uninitialized in this function
match_pdict.c: In function 'vmatch_XStringSet_XStringSet':
match_pdict.c:463: warning: 'ans_elt' may be used uninitialized in this function
match_pdict.c:463: note: 'ans_elt' was declared here
match_pdict.c: In function 'vmatch_PDict3Parts_XStringSet':
match_pdict.c:414: warning: 'ans_col' may be used uninitialized in this function
match_pdict.c:414: note: 'ans_col' was declared here
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c:641: warning: 'a_nice_max_nodeextbuf_nelt' defined but not used
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pdict_Twobit.c -o match_pdict_Twobit.o
match_pdict_Twobit.c: In function 'build_Twobit':
match_pdict_Twobit.c:125: warning: 'twobit_sign2pos' may be used uninitialized in this function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function 'match_ppheadtail0':
match_pdict_utils.c:664: warning: unused variable 'ncol'
match_pdict_utils.c: In function 'match_ppheadtail':
match_pdict_utils.c:722: warning: unused variable 'nelt'
match_pdict_utils.c: In function '_match_pdict_all_flanks':
match_pdict_utils.c:821: warning: unused variable 'subtotal_NFC'
match_pdict_utils.c:821: warning: unused variable 'total_NFC'
match_pdict_utils.c:820: warning: unused variable 'NFC'
match_pdict_utils.c:820: warning: unused variable 'nloci'
match_pdict_utils.c:820: warning: unused variable 'ndup'
match_pdict_utils.c: At top level:
match_pdict_utils.c:279: warning: 'match_headtail_by_loc' defined but not used
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_reporting.c -o match_reporting.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c matchprobes.c -o matchprobes.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c pmatchPattern.c -o pmatchPattern.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c replace_letter_at.c -o replace_letter_at.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c strutils.c -o strutils.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c translate.c -o translate.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c utils.c -o utils.o
utils.c: In function '_get_twobit_signature_at':
utils.c:210: warning: 'twobit_sign' may be used uninitialized in this function
utils.c: In function '_get_twobit_signature':
utils.c:196: warning: 'twobit_sign' may be used uninitialized in this function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c xscat.c -o xscat.o
xscat.c: In function 'XStringSet_xscat':
xscat.c:94: warning: 'ans_length' is used uninitialized in this function
xscat.c:70: warning: 'ans_element_type' may be used uninitialized in this function
xscat.c: In function 'XString_xscat':
xscat.c:36: warning: 'ans_length' is used uninitialized in this function
xscat.c:18: warning: 'ans_classname' may be used uninitialized in this function
gcc -arch x86_64 -std=gnu99 -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 XStringSet_class.o XStringSet_io.o XString_class.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_WCP.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 utils.o xscat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/Biostrings.buildbin-libdir/Biostrings/libs/x86_64

* DONE (Biostrings)


>>>>>>> 
>>>>>>> FIXING LINKS FOR Biostrings.buildbin-libdir/Biostrings/libs/x86_64/Biostrings.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgcc_s.1.dylib" "Biostrings.buildbin-libdir/Biostrings/libs/x86_64/Biostrings.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "Biostrings.buildbin-libdir/Biostrings/libs/x86_64/Biostrings.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.5.2.dylib" "Biostrings.buildbin-libdir/Biostrings/libs/x86_64/Biostrings.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "Biostrings.buildbin-libdir/Biostrings/libs/x86_64/Biostrings.so"