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Package 59/436HostnameOS / ArchBUILDCHECKBUILD BIN
Biostrings 2.19.11
H. Pages
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biostrings
Last Changed Rev: 53255 / Revision: 53255
Last Changed Date: 2011-02-24 11:16:43 -0800 (Thu, 24 Feb 2011)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ WARNINGS ] OK 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK  WARNINGS  OK 

Summary

Package: Biostrings
Version: 2.19.11
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biostrings_2.19.11.tar.gz
StartedAt: 2011-02-24 18:27:13 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 18:41:42 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 869.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Biostrings.Rcheck
Warnings: 1

Command output

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/Biostrings.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biostrings/DESCRIPTION’ ... OK
* this is package ‘Biostrings’ version ‘2.19.11’
* 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:
  XStringSet_io.c:319: warning: ‘loader_ext.cached_ans_elt.length’ is used uninitialized in this function
  XStringSet_io.c:319: warning: ‘loader_ext.cached_ans_elt.seq’ is used uninitialized in this function
  xscat.c:94: warning: ‘ans_length’ is used uninitialized in this function
  xscat.c:36: warning: ‘ans_length’ is used uninitialized in this function
See ‘/Users/biocbuild/bbs-2.8-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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 ... NOTE
.checkFormat: no visible binding for global variable ‘filepath’
* checking Rd files ... OK
* 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 Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
'library' or 'require' call not declared from: BSgenome.Hsapiens.UCSC.hg18
* 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 ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  ‘/Users/biocbuild/bbs-2.8-bioc/meat/Biostrings.Rcheck/00check.log’
for details

Biostrings.Rcheck/00install.out:

* installing *source* package ‘Biostrings’ ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c BAB_class.c -o BAB_class.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c BitMatrix.c -o BitMatrix.o
BitMatrix.c: In function ‘debug_BitMatrix’:
BitMatrix.c:382: warning: left shift count >= width of type
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function ‘SparseMIndex_endIndex’:
MIndex_class.c:192: warning: unused variable ‘poffsets_order’
MIndex_class.c: In function ‘_get_cachedMIndex_elt’:
MIndex_class.c:93: warning: ‘cached_iranges.end’ may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c SparseList_utils.c -o SparseList_utils.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function ‘new_XStringSet_from_CHARACTER’:
XStringSet_class.c:92: warning: ‘lkup_length’ may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c XStringSet_io.c -o XStringSet_io.o
XStringSet_io.c: In function ‘parse_FASTQ_file’:
XStringSet_io.c:546: warning: ‘load_record’ may be used uninitialized in this function
XStringSet_io.c: In function ‘read_fastq_in_XStringSet’:
XStringSet_io.c:510: warning: ‘loader_ext.lkup_length’ may be used uninitialized in this function
XStringSet_io.c:510: note: ‘loader_ext.lkup_length’ was declared here
XStringSet_io.c: In function ‘read_fasta_in_XStringSet’:
XStringSet_io.c:319: warning: ‘loader_ext.cached_ans_elt.length’ is used uninitialized in this function
XStringSet_io.c:319: warning: ‘loader_ext.cached_ans_elt.seq’ is used uninitialized in this function
XStringSet_io.c:166: warning: ‘loader_ext.lkup_length’ may be used uninitialized in this function
XStringSet_io.c:166: note: ‘loader_ext.lkup_length’ was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c XString_class.c -o XString_class.o
XString_class.c: In function ‘new_XString_from_CHARACTER’:
XString_class.c:162: warning: ‘lkup_length’ may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function ‘align_needwunsQS’:
align_needwunsQS.c:39: warning: ‘lkup_val’ may be used uninitialized in this function
align_needwunsQS.c:39: note: ‘lkup_val’ was declared here
align_needwunsQS.c:26: warning: ‘sc’ may be used uninitialized in this function
align_needwunsQS.c:26: note: ‘sc’ was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c align_utils.c -o align_utils.o
align_utils.c: In function ‘PairwiseAlignedFixedSubject_align_aligned’:
align_utils.c:223: warning: ‘indelStartSubject’ may be used uninitialized in this function
align_utils.c:223: warning: ‘indelWidthPattern’ may be used uninitialized in this function
align_utils.c:223: warning: ‘indelStartPattern’ may be used uninitialized in this function
align_utils.c:223: warning: ‘indelWidthSubject’ may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c extract_transcripts.c -o extract_transcripts.o
extract_transcripts.c: In function ‘tlocs2rlocs’:
extract_transcripts.c:165: warning: ‘start’ may be used uninitialized in this function
extract_transcripts.c:165: note: ‘start’ was declared here
extract_transcripts.c:165: warning: ‘end’ may be used uninitialized in this function
extract_transcripts.c:165: note: ‘end’ was declared here
extract_transcripts.c:243: warning: ‘nlocs’ may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c find_palindromes.c -o find_palindromes.o
find_palindromes.c: In function ‘find_palindromes’:
find_palindromes.c:26: warning: ‘letter0’ may be used uninitialized in this function
find_palindromes.c:26: note: ‘letter0’ was declared here
find_palindromes.c:25: warning: ‘all_letter0’ may be used uninitialized in this function
find_palindromes.c:25: note: ‘all_letter0’ was declared here
find_palindromes.c:82: warning: ‘letter0’ may be used uninitialized in this function
find_palindromes.c:82: note: ‘letter0’ was declared here
find_palindromes.c:81: warning: ‘lkup_val’ may be used uninitialized in this function
find_palindromes.c:81: note: ‘lkup_val’ was declared here
find_palindromes.c:81: warning: ‘all_letter0’ may be used uninitialized in this function
find_palindromes.c:81: note: ‘all_letter0’ was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c gtestsim.c -o gtestsim.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c inject_code.c -o inject_code.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c io_utils.c -o io_utils.o
io_utils.c: In function ‘open_input_file’:
io_utils.c:70: warning: unused variable ‘buf’
io_utils.c:69: warning: unused variable ‘ret’
io_utils.c: In function ‘new_input_ExternalFilePtr’:
io_utils.c:68: warning: ‘fp’ may be used uninitialized in this function
io_utils.c:68: note: ‘fp’ was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c letter_frequency.c -o letter_frequency.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c lowlevel_matching.c -o lowlevel_matching.o
lowlevel_matching.c: In function ‘XStringSet_vmatch_pattern_at’:
lowlevel_matching.c:586: warning: ‘ans’ may be used uninitialized in this function
lowlevel_matching.c:584: warning: ‘ans_nrow’ may be used uninitialized in this function
lowlevel_matching.c:584: warning: ‘ans_elt’ may be used uninitialized in this function
lowlevel_matching.c: In function ‘XString_match_pattern_at’:
lowlevel_matching.c:536: warning: ‘ans’ may be used uninitialized in this function
lowlevel_matching.c:534: warning: ‘ans_elt’ may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_BOC.c -o match_BOC.o
match_BOC.c: In function ‘BOC_preprocess’:
match_BOC.c:82: warning: overflow in implicit constant conversion
match_BOC.c: In function ‘BOC_exact_search’:
match_BOC.c:331: warning: label ‘continue0’ defined but not used
match_BOC.c:268: warning: unused variable ‘noffsets’
match_BOC.c:268: warning: unused variable ‘offsets’
match_BOC.c:268: warning: unused variable ‘j’
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_BOC2.c -o match_BOC2.o
match_BOC2.c: In function ‘BOC2_exact_search’:
match_BOC2.c:288: warning: label ‘continue0’ defined but not used
match_BOC2.c:234: warning: unused variable ‘noffsets’
match_BOC2.c:234: warning: unused variable ‘offsets’
match_BOC2.c:234: warning: unused variable ‘j’
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_PWM.c -o match_PWM.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_WCP.c -o match_WCP.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pattern.c -o match_pattern.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
match_pattern_boyermoore.c: In function ‘_match_pattern_boyermoore’:
match_pattern_boyermoore.c:401: warning: ‘c’ may be used uninitialized in this function
match_pattern_boyermoore.c:399: warning: ‘j1’ may be used uninitialized in this function
match_pattern_boyermoore.c:399: warning: ‘i2’ may be used uninitialized in this function
match_pattern_boyermoore.c:399: warning: ‘i1’ may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pattern_indels.c -o match_pattern_indels.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pdict.c -o match_pdict.o
match_pdict.c: In function ‘init_vcount_collapsed_ans’:
match_pdict.c:110: warning: ‘ans_length’ may be used uninitialized in this function
match_pdict.c: In function ‘vmatch_XStringSet_XStringSet’:
match_pdict.c:458: warning: ‘ans_elt’ may be used uninitialized in this function
match_pdict.c:458: note: ‘ans_elt’ was declared here
match_pdict.c: In function ‘vmatch_PDict3Parts_XStringSet’:
match_pdict.c:410: warning: ‘ans_col’ may be used uninitialized in this function
match_pdict.c:410: note: ‘ans_col’ was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c:641: warning: ‘a_nice_max_nodeextbuf_nelt’ defined but not used
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pdict_Twobit.c -o match_pdict_Twobit.o
match_pdict_Twobit.c: In function ‘build_Twobit’:
match_pdict_Twobit.c:125: warning: ‘twobit_sign2pos’ may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function ‘match_ppheadtail0’:
match_pdict_utils.c:653: warning: unused variable ‘ncol’
match_pdict_utils.c: In function ‘_match_pdict_all_flanks’:
match_pdict_utils.c:806: warning: unused variable ‘subtotal_NFC’
match_pdict_utils.c:806: warning: unused variable ‘total_NFC’
match_pdict_utils.c:805: warning: unused variable ‘NFC’
match_pdict_utils.c:805: warning: unused variable ‘nloci’
match_pdict_utils.c:805: warning: unused variable ‘ndup’
match_pdict_utils.c: At top level:
match_pdict_utils.c:272: warning: ‘match_headtail_by_loc’ defined but not used
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c match_reporting.c -o match_reporting.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c matchprobes.c -o matchprobes.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c pmatchPattern.c -o pmatchPattern.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c replace_letter_at.c -o replace_letter_at.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c strutils.c -o strutils.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c translate.c -o translate.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c utils.c -o utils.o
utils.c: In function ‘_get_twobit_signature_at’:
utils.c:210: warning: ‘twobit_sign’ may be used uninitialized in this function
utils.c: In function ‘_get_twobit_signature’:
utils.c:196: warning: ‘twobit_sign’ may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c xscat.c -o xscat.o
xscat.c: In function ‘XStringSet_xscat’:
xscat.c:94: warning: ‘ans_length’ is used uninitialized in this function
xscat.c:70: warning: ‘ans_element_type’ may be used uninitialized in this function
xscat.c: In function ‘XString_xscat’:
xscat.c:36: warning: ‘ans_length’ is used uninitialized in this function
xscat.c:18: warning: ‘ans_classname’ may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o SparseList_utils.o XStringSet_class.o XStringSet_io.o XString_class.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o extract_transcripts.o find_palindromes.o gtestsim.o inject_code.o io_utils.o letter_frequency.o lowlevel_matching.o match_BOC.o match_BOC2.o match_PWM.o match_WCP.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o replace_letter_at.o strutils.o translate.o utils.o xscat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/Biostrings.Rcheck/Biostrings/libs/i386
** R
** data
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'

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

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Creating a new generic function for "setequal" in "Biostrings"
Creating a new generic function for "ls" in "Biostrings"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (Biostrings)

Biostrings.Rcheck/Biostrings-Ex.timings:

nameusersystemelapsed
AAString-class0.0100.0010.011
AMINO_ACID_CODE0.0040.0000.004
AlignedXStringSet-class0.2420.0080.250
DNAString-class0.0040.0010.004
FASTA-io-legacy13.656 2.11517.159
GENETIC_CODE0.0070.0010.008
HNF4alpha0.0830.0010.085
IUPAC_CODE_MAP0.0140.0000.015
MIndex-class000
MaskedXString-class0.6630.0360.917
MultipleAlignment-class4.0740.0524.187
PDict-class6.2240.5916.900
PairwiseAlignedXStringSet-class0.3540.0030.358
QualityScaledXStringSet-class0.0530.0010.053
RNAString-class0.0150.0010.016
XString-class0.0150.0010.016
XStringQuality-class0.1400.0020.143
XStringSet-class15.542 1.90517.580
XStringSet-io7.7191.3669.423
XStringSetList-class0.1240.0060.137
XStringViews-class0.3600.0130.390
XStringViews-constructor0.0670.0020.073
align-utils0.1550.0140.175
basecontent0.0060.0000.007
chartr1.4680.1041.634
complementSeq0.0790.0080.093
detail1.5130.0571.747
dinucleotideFrequencyTest0.0430.0100.055
extractTranscripts0.5250.0800.641
findPalindromes11.633 0.29712.742
gregexpr20.0040.0010.004
injectHardMask0.1050.0050.112
letter0.0260.0020.028
letterFrequency3.8530.5174.468
longestConsecutive0.0010.0000.000
lowlevel-matching1.9380.1902.144
maskMotif2.6190.2043.173
match-utils0.1040.0190.124
matchLRPatterns1.1190.0661.242
matchPDict-exact449.078 7.436459.447
matchPDict-inexact62.574 2.45965.599
matchPWM5.1270.0545.242
matchPattern5.8600.1756.063
matchProbePair2.8880.0622.962
matchprobes1.4740.0351.523
misc0.0260.0020.029
needwunsQS0.0000.0000.001
nucleotideFrequency2.7840.1903.020
pairwiseAlignment1.7120.7222.452
phiX174Phage1.3490.4441.811
pid0.7100.3791.123
replaceLetterAt2.1100.5232.655
reverse4.2510.7925.117
reverseSeq0.0610.0010.062
stringDist14.136 0.36714.574
substitution_matrices1.0470.4821.550
toComplex0.0040.0000.004
translate2.0350.0082.050
trimLRPatterns0.3680.0020.372
xscat4.9390.4145.384
yeastSEQCHR10.0060.0010.007