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Package 52/354HostnameOS / ArchBUILDCHECKBUILD BIN
Biostrings 2.15.9
H. Pages
Bioconductor Changelog
Snapshot Date: 2009-12-07 11:32:00 -0800 (Mon, 07 Dec 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biostrings
Last Changed Rev: 43249 / Revision: 43434
Last Changed Date: 2009-11-24 22:25:48 -0800 (Tue, 24 Nov 2009)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386 [ OK ] WARNINGS  OK 
Package: Biostrings
Version: 2.15.9
Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD build Biostrings
StartedAt: 2009-12-07 13:25:42 -0800 (Mon, 07 Dec 2009)
EndedAt: 2009-12-07 13:31:15 -0800 (Mon, 07 Dec 2009)
EllapsedTime: 333.4 seconds
RetCode: 0
Status: OK
PackageFile: Biostrings_2.15.9.tar.gz
PackageFileSize: 978.5 KiB

Command output

* checking for file 'Biostrings/DESCRIPTION' ... OK
* preparing 'Biostrings':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* installing *source* package ‘Biostrings’ ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c BAB_class.c -o BAB_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c BitMatrix.c -o BitMatrix.o
BitMatrix.c: In function ‘debug_BitMatrix’:
BitMatrix.c:382: warning: left shift count >= width of type
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c XStringSet_class.c -o XStringSet_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c XStringSet_io.c -o XStringSet_io.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c XString_class.c -o XString_class.o
XString_class.c:117: warning: ‘new_RoSeqs_from_XString’ defined but not used
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c align_utils.c -o align_utils.o
align_utils.c: In function ‘PairwiseAlignedFixedSubject_align_aligned’:
align_utils.c:225: warning: ‘indelWidthSubject’ may be used uninitialized in this function
align_utils.c:225: warning: ‘indelStartSubject’ may be used uninitialized in this function
align_utils.c:225: warning: ‘indelWidthPattern’ may be used uninitialized in this function
align_utils.c:225: warning: ‘indelStartPattern’ may be used uninitialized in this function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c extract_transcripts.c -o extract_transcripts.o
extract_transcripts.c: In function ‘tlocs2rlocs’:
extract_transcripts.c:224: warning: ‘nlocs’ may be used uninitialized in this function
extract_transcripts.c:149: warning: ‘end’ may be used uninitialized in this function
extract_transcripts.c:149: note: ‘end’ was declared here
extract_transcripts.c:149: warning: ‘start’ may be used uninitialized in this function
extract_transcripts.c:149: note: ‘start’ was declared here
extract_transcripts.c: In function ‘extract_transcripts’:
extract_transcripts.c:211: warning: passing argument 1 of ‘copy_transcript’ discards qualifiers from pointer target type
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c find_palindromes.c -o find_palindromes.o
find_palindromes.c: In function ‘find_palindromes’:
find_palindromes.c:25: warning: ‘letter0’ may be used uninitialized in this function
find_palindromes.c:25: note: ‘letter0’ was declared here
find_palindromes.c:24: warning: ‘all_letter0’ may be used uninitialized in this function
find_palindromes.c:24: note: ‘all_letter0’ was declared here
find_palindromes.c:79: warning: ‘letter0’ may be used uninitialized in this function
find_palindromes.c:79: note: ‘letter0’ was declared here
find_palindromes.c:78: warning: ‘lkup_val’ may be used uninitialized in this function
find_palindromes.c:78: note: ‘lkup_val’ was declared here
find_palindromes.c:78: warning: ‘all_letter0’ may be used uninitialized in this function
find_palindromes.c:78: note: ‘all_letter0’ was declared here
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c gtestsim.c -o gtestsim.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c inject_code.c -o inject_code.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c letter_frequency.c -o letter_frequency.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c lowlevel_matching.c -o lowlevel_matching.o
lowlevel_matching.c: In function ‘_nedit_for_Proffset’:
lowlevel_matching.c:285: warning: unused variable ‘Pc’
lowlevel_matching.c:284: warning: unused variable ‘j’
lowlevel_matching.c:284: warning: unused variable ‘jmin’
lowlevel_matching.c:284: warning: unused variable ‘iplus1’
lowlevel_matching.c:284: warning: unused variable ‘i’
lowlevel_matching.c:284: warning: unused variable ‘b’
lowlevel_matching.c:284: warning: unused variable ‘B’
lowlevel_matching.c:283: warning: unused variable ‘row_length’
lowlevel_matching.c:283: warning: unused variable ‘curr_row’
lowlevel_matching.c:283: warning: unused variable ‘prev_row’
lowlevel_matching.c:283: warning: unused variable ‘max_nedit_plus1’
lowlevel_matching.c: In function ‘XStringSet_vmatch_pattern_at’:
lowlevel_matching.c:485: warning: ‘ans_nrow’ may be used uninitialized in this function
lowlevel_matching.c:485: warning: ‘ans_elt’ may be used uninitialized in this function
lowlevel_matching.c:486: warning: ‘ans’ may be used uninitialized in this function
lowlevel_matching.c: In function ‘XString_match_pattern_at’:
lowlevel_matching.c:438: warning: ‘ans’ may be used uninitialized in this function
lowlevel_matching.c:437: warning: ‘ans_elt’ may be used uninitialized in this function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_BOC.c -o match_BOC.o
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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_PWM.c -o match_PWM.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_WCP.c -o match_WCP.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_pattern.c -o match_pattern.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_pattern_indels.c -o match_pattern_indels.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_pdict.c -o match_pdict.o
match_pdict.c: In function ‘XStringSet_vmatch_pdict’:
match_pdict.c:263: warning: ‘ans_length’ may be used uninitialized in this function
match_pdict.c:263: note: ‘ans_length’ was declared here
match_pdict.c:320: warning: ‘ans’ may be used uninitialized in this function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_pdict_ACtree.c -o match_pdict_ACtree.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c:593: warning: ‘a_nice_max_nodeextbuf_nelt’ defined but not used
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function ‘match_ppheadtail0’:
match_pdict_utils.c:836: warning: unused variable ‘ncol’
match_pdict_utils.c: In function ‘_match_pdict_all_flanks’:
match_pdict_utils.c:989: warning: unused variable ‘subtotal_NFC’
match_pdict_utils.c:989: warning: unused variable ‘total_NFC’
match_pdict_utils.c:988: warning: unused variable ‘NFC’
match_pdict_utils.c:988: warning: unused variable ‘nloci’
match_pdict_utils.c:988: warning: unused variable ‘ndup’
match_pdict_utils.c: At top level:
match_pdict_utils.c:464: warning: ‘match_headtail_by_loc’ defined but not used
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_reporting.c -o match_reporting.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c matchprobes.c -o matchprobes.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c replace_letter_at.c -o replace_letter_at.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c strutils.c -o strutils.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c utils.c -o utils.o
utils.c: In function ‘_get_twobit_signature_at’:
utils.c:240: warning: ‘twobit_sign’ may be used uninitialized in this function
utils.c: In function ‘_get_twobit_signature’:
utils.c:226: warning: ‘twobit_sign’ may be used uninitialized in this function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c xscat.c -o xscat.o
xscat.c: In function ‘XStringSet_xscat’:
xscat.c:86: warning: ‘ans_length’ is used uninitialized in this function
xscat.c:63: warning: ‘ans_xsbaseclassname’ may be used uninitialized in this function
xscat.c: In function ‘XString_xscat’:
xscat.c:36: warning: ‘ans_classname’ is used uninitialized in this function
xscat.c:36: warning: ‘ans_length’ is used uninitialized in this function
gcc-4.2 -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 extract_transcripts.o find_palindromes.o gtestsim.o inject_code.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_ACtree.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 utils.o xscat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c BAB_class.c -o BAB_class.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c BitMatrix.c -o BitMatrix.o
BitMatrix.c: In function ‘debug_BitMatrix’:
BitMatrix.c:382: warning: left shift count >= width of type
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c MIndex_class.c -o MIndex_class.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c SparseList_utils.c -o SparseList_utils.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c XStringSet_class.c -o XStringSet_class.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c XStringSet_io.c -o XStringSet_io.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c XString_class.c -o XString_class.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c align_needwunsQS.c -o align_needwunsQS.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c align_utils.c -o align_utils.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c extract_transcripts.c -o extract_transcripts.o
extract_transcripts.c: In function ‘extract_transcripts’:
extract_transcripts.c:211: warning: passing argument 1 of ‘copy_transcript’ discards qualifiers from pointer target type
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c find_palindromes.c -o find_palindromes.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c gtestsim.c -o gtestsim.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c inject_code.c -o inject_code.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c letter_frequency.c -o letter_frequency.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c lowlevel_matching.c -o lowlevel_matching.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c match_BOC.c -o match_BOC.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c match_BOC2.c -o match_BOC2.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c match_PWM.c -o match_PWM.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c match_WCP.c -o match_WCP.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c match_pattern.c -o match_pattern.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c match_pattern_indels.c -o match_pattern_indels.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c match_pdict.c -o match_pdict.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c match_pdict_ACtree.c -o match_pdict_ACtree.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c match_pdict_Twobit.c -o match_pdict_Twobit.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c match_pdict_utils.c -o match_pdict_utils.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c match_reporting.c -o match_reporting.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c matchprobes.c -o matchprobes.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c pmatchPattern.c -o pmatchPattern.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c replace_letter_at.c -o replace_letter_at.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c strutils.c -o strutils.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c utils.c -o utils.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -c xscat.c -o xscat.o
gcc-4.2 -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 extract_transcripts.o find_palindromes.o gtestsim.o inject_code.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_ACtree.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 utils.o xscat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c BAB_class.c -o BAB_class.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c BitMatrix.c -o BitMatrix.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -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-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c XStringSet_class.c -o XStringSet_class.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c XStringSet_io.c -o XStringSet_io.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c XString_class.c -o XString_class.o
XString_class.c:117: warning: ‘new_RoSeqs_from_XString’ defined but not used
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -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-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c align_utils.c -o align_utils.o
align_utils.c: In function ‘PairwiseAlignedFixedSubject_align_aligned’:
align_utils.c:225: warning: ‘indelWidthSubject’ may be used uninitialized in this function
align_utils.c:225: warning: ‘indelStartSubject’ may be used uninitialized in this function
align_utils.c:225: warning: ‘indelWidthPattern’ may be used uninitialized in this function
align_utils.c:225: warning: ‘indelStartPattern’ may be used uninitialized in this function
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c extract_transcripts.c -o extract_transcripts.o
extract_transcripts.c: In function ‘tlocs2rlocs’:
extract_transcripts.c:149: warning: ‘end’ may be used uninitialized in this function
extract_transcripts.c:149: note: ‘end’ was declared here
extract_transcripts.c:149: warning: ‘start’ may be used uninitialized in this function
extract_transcripts.c:149: note: ‘start’ was declared here
extract_transcripts.c:224: warning: ‘nlocs’ may be used uninitialized in this function
extract_transcripts.c: In function ‘extract_transcripts’:
extract_transcripts.c:211: warning: passing argument 1 of ‘copy_transcript’ discards qualifiers from pointer target type
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c find_palindromes.c -o find_palindromes.o
find_palindromes.c: In function ‘find_palindromes’:
find_palindromes.c:25: warning: ‘letter0’ may be used uninitialized in this function
find_palindromes.c:25: note: ‘letter0’ was declared here
find_palindromes.c:24: warning: ‘all_letter0’ may be used uninitialized in this function
find_palindromes.c:24: note: ‘all_letter0’ was declared here
find_palindromes.c:79: warning: ‘letter0’ may be used uninitialized in this function
find_palindromes.c:79: note: ‘letter0’ was declared here
find_palindromes.c:78: warning: ‘lkup_val’ may be used uninitialized in this function
find_palindromes.c:78: note: ‘lkup_val’ was declared here
find_palindromes.c:78: warning: ‘all_letter0’ may be used uninitialized in this function
find_palindromes.c:78: note: ‘all_letter0’ was declared here
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c gtestsim.c -o gtestsim.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c inject_code.c -o inject_code.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c letter_frequency.c -o letter_frequency.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c lowlevel_matching.c -o lowlevel_matching.o
lowlevel_matching.c: In function ‘_nedit_for_Proffset’:
lowlevel_matching.c:285: warning: unused variable ‘Pc’
lowlevel_matching.c:284: warning: unused variable ‘j’
lowlevel_matching.c:284: warning: unused variable ‘jmin’
lowlevel_matching.c:284: warning: unused variable ‘iplus1’
lowlevel_matching.c:284: warning: unused variable ‘i’
lowlevel_matching.c:284: warning: unused variable ‘b’
lowlevel_matching.c:284: warning: unused variable ‘B’
lowlevel_matching.c:283: warning: unused variable ‘row_length’
lowlevel_matching.c:283: warning: unused variable ‘curr_row’
lowlevel_matching.c:283: warning: unused variable ‘prev_row’
lowlevel_matching.c:283: warning: unused variable ‘max_nedit_plus1’
lowlevel_matching.c: In function ‘XStringSet_vmatch_pattern_at’:
lowlevel_matching.c:486: warning: ‘ans’ may be used uninitialized in this function
lowlevel_matching.c:485: warning: ‘ans_nrow’ may be used uninitialized in this function
lowlevel_matching.c:485: warning: ‘ans_elt’ may be used uninitialized in this function
lowlevel_matching.c: In function ‘XString_match_pattern_at’:
lowlevel_matching.c:438: warning: ‘ans’ may be used uninitialized in this function
lowlevel_matching.c:437: warning: ‘ans_elt’ may be used uninitialized in this function
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_BOC.c -o match_BOC.o
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-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -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-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_PWM.c -o match_PWM.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_WCP.c -o match_WCP.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_pattern.c -o match_pattern.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -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-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_pattern_indels.c -o match_pattern_indels.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_pdict.c -o match_pdict.o
match_pdict.c: In function ‘XStringSet_vmatch_pdict’:
match_pdict.c:263: warning: ‘ans_length’ may be used uninitialized in this function
match_pdict.c:263: note: ‘ans_length’ was declared here
match_pdict.c:320: warning: ‘ans’ may be used uninitialized in this function
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_pdict_ACtree.c -o match_pdict_ACtree.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c:593: warning: ‘a_nice_max_nodeextbuf_nelt’ defined but not used
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -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-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function ‘match_ppheadtail0’:
match_pdict_utils.c:836: warning: unused variable ‘ncol’
match_pdict_utils.c: In function ‘_match_pdict_all_flanks’:
match_pdict_utils.c:989: warning: unused variable ‘subtotal_NFC’
match_pdict_utils.c:989: warning: unused variable ‘total_NFC’
match_pdict_utils.c:988: warning: unused variable ‘NFC’
match_pdict_utils.c:988: warning: unused variable ‘nloci’
match_pdict_utils.c:988: warning: unused variable ‘ndup’
match_pdict_utils.c: At top level:
match_pdict_utils.c:464: warning: ‘match_headtail_by_loc’ defined but not used
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c match_reporting.c -o match_reporting.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c matchprobes.c -o matchprobes.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c replace_letter_at.c -o replace_letter_at.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c strutils.c -o strutils.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c utils.c -o utils.o
utils.c: In function ‘_get_twobit_signature_at’:
utils.c:240: warning: ‘twobit_sign’ may be used uninitialized in this function
utils.c: In function ‘_get_twobit_signature’:
utils.c:226: warning: ‘twobit_sign’ may be used uninitialized in this function
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -c xscat.c -o xscat.o
xscat.c: In function ‘XStringSet_xscat’:
xscat.c:86: warning: ‘ans_length’ is used uninitialized in this function
xscat.c:63: warning: ‘ans_xsbaseclassname’ may be used uninitialized in this function
xscat.c: In function ‘XString_xscat’:
xscat.c:36: warning: ‘ans_classname’ is used uninitialized in this function
xscat.c:36: warning: ‘ans_length’ is used uninitialized in this function
gcc-4.2 -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 extract_transcripts.o find_palindromes.o gtestsim.o inject_code.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_ACtree.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 utils.o xscat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** data
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'


	The following object(s) are masked from package:base :

	 Map,
	 cbind,
	 mapply,
	 order,
	 pmax,
	 pmax.int,
	 pmin,
	 pmin.int,
	 rbind,
	 rep.int,
	 table 

Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "XString" no definition for class: “AsIs”
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "XStringSet" no definition for class: “AsIs”
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "XStringSet" no definition for class: “probetable”
Creating a new generic function for "setequal" in "Biostrings"
Creating a new generic function for "is.unsorted" in "Biostrings"
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "BStringViews" no definition for class: “file”
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "consensusString" no definition for class: “BStringViews”
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "consensusString" no definition for class: “DNAStringViews”
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "consensusString" no definition for class: “RNAStringViews”
Creating a new generic function for "ls" in "Biostrings"
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "PDict" no definition for class: “AsIs”
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "PDict" no definition for class: “probetable”
** help
*** installing help indices
** building package indices ...
* DONE (Biostrings)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'Biostrings_2.15.9.tar.gz'