Biostrings 2.14.12
H. Pages
| Snapshot Date: 2010-04-02 23:28:25 -0700 (Fri, 02 Apr 2010) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/Biostrings | | Last Changed Rev: 44488 / Revision: 45705 | | Last Changed Date: 2010-02-03 21:52:26 -0800 (Wed, 03 Feb 2010) |
| wilson2 | 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 | ERROR | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | [ ERROR ] | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.5-bioc/meat/Biostrings.Rcheck'
* using R version 2.10.1 Patched (2009-12-14 r50738)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.14.12'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Biostrings' can be installed ... WARNING
Found the following significant warnings:
extract_transcripts.c:211: warning: passing argument 1 of ‘copy_transcript’ discards qualifiers from pointer target type
xscat.c:86: warning: ‘ans_length’ is used uninitialized in this function
xscat.c:36: warning: ‘ans_classname’ is used uninitialized in this function
xscat.c:36: warning: ‘ans_length’ is used uninitialized in this function
extract_transcripts.c:211: warning: passing argument 1 of ‘copy_transcript’ discards qualifiers from pointer target type
extract_transcripts.c:211: warning: passing argument 1 of ‘copy_transcript’ discards qualifiers from pointer target type
xscat.c:86: warning: ‘ans_length’ is used uninitialized in this function
xscat.c:36: warning: ‘ans_classname’ is used uninitialized in this function
xscat.c:36: warning: ‘ans_length’ is used uninitialized in this function
See '/Users/biocbuild/bbs-2.5-bioc/meat/Biostrings.Rcheck/00install.out' for details.
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
prepare_Rd: InDel-class.Rd:50-51: Dropping empty section \examples
prepare_Rd: WCP.Rd:32-33: Dropping empty section \details
prepare_Rd: WCP.Rd:42-43: Dropping empty section \examples
prepare_Rd: XKeySortedData.Rd:39-40: Dropping empty section \details
prepare_Rd: XKeySortedData.Rd:49-50: Dropping empty section \examples
prepare_Rd: XKeySortedDataList.Rd:30-31: Dropping empty section \details
prepare_Rd: XKeySortedDataList.Rd:40-41: Dropping empty section \examples
prepare_Rd: matchWCP.Rd:70-71: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... ERROR
Running examples in 'Biostrings-Ex.R' failed.
The error most likely occurred in:
> ### * translate
>
> flush(stderr()); flush(stdout())
>
> ### Name: translate
> ### Title: DNA/RNA transcription and translation
> ### Aliases: transcribe cDNA dna2rna rna2dna codons codons,DNAString-method
> ### codons,RNAString-method codons,MaskedDNAString-method
> ### codons,MaskedRNAString-method translate translate,DNAString-method
> ### translate,RNAString-method translate,DNAStringSet-method
> ### translate,RNAStringSet-method translate,MaskedDNAString-method
> ### translate,MaskedRNAString-method
> ### Keywords: methods manip
>
> ### ** Examples
>
> file <- system.file("extdata", "someORF.fa", package="Biostrings")
> x <- read.DNAStringSet(file)
> x
A DNAStringSet instance of length 7
width seq names
[1] 5573 ACTTGTAAATATATCTTTTATTT...CTTATCGACCTTATTGTTGATAT YAL001C TFC3 SGDI...
[2] 5825 TTCCAAGGCCGATGAATTCGACT...AGTAAATTTTTTTCTATTCTCTT YAL002W VPS8 SGDI...
[3] 2987 CTTCATGTCAGCCTGCACTTCTG...TGGTACTCATGTAGCTGCCTCAT YAL003W EFB1 SGDI...
[4] 3929 CACTCATATCGGGGGTCTTACTT...TGTCCCGAAACACGAAAAAGTAC YAL005C SSA1 SGDI...
[5] 2648 AGAGAAAGAGTTTCACTTCTTGA...ATATAATTTATGTGTGAACATAG YAL007C ERP2 SGDI...
[6] 2597 GTGTCCGGGCCTCGCAGGCGTTC...AAGTTTTGGCAGAATGTACTTTT YAL008W FUN14 SGD...
[7] 2780 CAAGATAATGTCAAAGTTAGTGG...GCTAAGGAAGAAAAAAAAATCAC YAL009W SPO7 SGDI...
>
> ## The first and last 1000 nucleotides are not part of the ORFs:
> x <- DNAStringSet(x, start=1001, end=-1001)
>
> ## Before calling translate() on an ORF, we need to mask the introns
> ## if any. We can get this information fron the SGD database
> ## (http://www.yeastgenome.org/).
> ## According to SGD, the 1st ORF (YAL001C) has an intron at 71..160
> ## (see http://db.yeastgenome.org/cgi-bin/locus.pl?locus=YAL001C)
> y1 <- x[[1]]
> mask1 <- Mask(length(y1), start=71, end=160)
> masks(y1) <- mask1
> y1
3573-letter "MaskedDNAString" instance (# for masking)
seq: ATGGTACTGACGATTTATCCTGACGAACTCGTACAA...AATCATAATTGGTATTCTATATATGAATCTACATAA
masks:
maskedwidth maskedratio active
1 90 0.02518892 TRUE
> translate(y1)
1161-letter "AAString" instance
seq: MVLTIYPDELVQIVSDKIASNKGKITLNQLWDISGK...ISEICKWLLERQVLITTDFDGYWVNHNWYSIYEST*
>
> ## Codons
> codons(y1)
Views on a 3573-letter DNAString subject
subject: ATGGTACTGACGATTTATCCTGACGAACTCGTAC...TCATAATTGGTATTCTATATATGAATCTACATAA
views:
start end width
[1] 1 3 3 [ATG]
[2] 4 6 3 [GTA]
[3] 7 9 3 [CTG]
[4] 10 12 3 [ACG]
[5] 13 15 3 [ATT]
[6] 16 18 3 [TAT]
[7] 19 21 3 [CCT]
[8] 22 24 3 [GAC]
[9] 25 27 3 [GAA]
... ... ... ... ...
[1153] 3547 3549 3 [TGG]
[1154] 3550 3552 3 [TAT]
[1155] 3553 3555 3 [TCT]
[1156] 3556 3558 3 [ATA]
[1157] 3559 3561 3 [TAT]
[1158] 3562 3564 3 [GAA]
[1159] 3565 3567 3 [TCT]
[1160] 3568 3570 3 [ACA]
[1161] 3571 3573 3 [TAA]
> which(width(codons(y1)) != 3)
[1] 24
> codons(y1)[20:28]
Error in assign(".defined", method@defined, envir = envir) :
formal argument "envir" matched by multiple actual arguments
Calls: codons ... switch -> xsbasetype -> loadMethod -> loadMethod -> assign
Execution halted
* install options are ' --no-html'
* installing *source* package ‘Biostrings’ ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/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 method for ‘XString’ with signature ‘"AsIs"’: no definition for class "AsIs"
Warning: in method for ‘XStringSet’ with signature ‘"AsIs"’: no definition for class "AsIs"
Warning: in method for ‘XStringSet’ with signature ‘"probetable"’: 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 method for ‘BStringViews’ with signature ‘"file"’: no definition for class "file"
Warning: in method for ‘consensusString’ with signature ‘"BStringViews"’: no definition for class "BStringViews"
Warning: in method for ‘consensusString’ with signature ‘"DNAStringViews"’: no definition for class "DNAStringViews"
Warning: in method for ‘consensusString’ with signature ‘"RNAStringViews"’: no definition for class "RNAStringViews"
Creating a new generic function for "ls" in "Biostrings"
Warning: in method for ‘PDict’ with signature ‘"AsIs"’: no definition for class "AsIs"
Warning: in method for ‘PDict’ with signature ‘"probetable"’: no definition for class "probetable"
** help
*** installing help indices
** building package indices ...
* DONE (Biostrings)