BioC 2.12: CHECK report for Biostrings on petty

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.27.12'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'Rmpi'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'Biostrings' can be installed ... [26s/27s] WARNING
Found the following significant warnings:
  XStringSet_io.c:368: warning: 'loader_ext.cached_ans_elt.length' is used uninitialized in this function
  XStringSet_io.c:368: 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-2.12-bioc/meat/Biostrings.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object '/Users/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck/00_pkg_src/Biostrings/man/MaskedXString-class.Rd':
  '[IRanges]{Ranges-utils}'

Missing link or links in documentation object '/Users/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck/00_pkg_src/Biostrings/man/MultipleAlignment-class.Rd':
  '[IRanges:Ranges-utils]{narrow}'

Missing link or links in documentation object '/Users/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck/00_pkg_src/Biostrings/man/XStringViews-class.Rd':
  '[IRanges:IRanges-setops]{gaps}'

See the information in section 'Cross-references' of the 'Writing R
Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'twoWayAlphabetFrequency'
Undocumented S4 methods:
  generic 'splitAsListReturnedClass' and siglist 'AAStringSet'
  generic 'splitAsListReturnedClass' and siglist 'BStringSet'
  generic 'splitAsListReturnedClass' and siglist 'DNAStringSet'
  generic 'splitAsListReturnedClass' and siglist 'RNAStringSet'
  generic 'twoWayAlphabetFrequency' and siglist 'XString,XString'
  generic 'twoWayAlphabetFrequency' and siglist 'XString,XStringSet'
  generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XString'
  generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XStringSet'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [573s/575s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
matchPDict-exact      371.104  5.881 377.197
matchPDict-inexact     63.138  2.173  65.421
stringDist             16.351  0.273  16.636
XStringSet-class       12.717  1.943  14.757
findPalindromes        10.933  0.129  11.063
XStringSet-io           7.745  1.289   9.128
PDict-class             7.970  0.545   8.570
XStringSet-comparison   5.398  1.385   6.810
matchPattern            5.316  0.253   5.577
matchPWM                5.336  0.095   5.433
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 3 warnings.
NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck/00check.log'
for details.

* installing *source* package 'Biostrings' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c BAB_class.c -o BAB_class.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c BitMatrix.c -o BitMatrix.o
BitMatrix.c: In function 'debug_BitMatrix':
BitMatrix.c:382: warning: left shift count >= width of type
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function 'SparseMIndex_endIndex':
MIndex_class.c:192: warning: unused variable 'poffsets_order'
MIndex_class.c: In function '_get_cachedMIndex_elt':
MIndex_class.c:93: warning: 'cached_iranges.end' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c SparseList_utils.c -o SparseList_utils.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function 'new_XStringSet_from_CHARACTER':
XStringSet_class.c:92: warning: 'lkup_length' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/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:594: warning: 'load_record' may be used uninitialized in this function
XStringSet_io.c: In function 'read_fastq_in_XStringSet':
XStringSet_io.c:558: warning: 'loader_ext.lkup_length' may be used uninitialized in this function
XStringSet_io.c:558: note: 'loader_ext.lkup_length' was declared here
XStringSet_io.c: In function 'fasta_info':
XStringSet_io.c:113: warning: 'loader.lkup_length' may be used uninitialized in this function
XStringSet_io.c:113: note: 'loader.lkup_length' was declared here
XStringSet_io.c: In function 'read_fasta_in_XStringSet':
XStringSet_io.c:368: warning: 'loader_ext.cached_ans_elt.length' is used uninitialized in this function
XStringSet_io.c:368: warning: 'loader_ext.cached_ans_elt.seq' is used uninitialized in this function
XStringSet_io.c:177: warning: 'loader.lkup_length' may be used uninitialized in this function
XStringSet_io.c:177: note: 'loader.lkup_length' was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c XString_class.c -o XString_class.o
XString_class.c: In function 'new_XString_from_CHARACTER':
XString_class.c:162: warning: 'lkup_length' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function 'align_needwunsQS':
align_needwunsQS.c:39: warning: 'lkup_val' may be used uninitialized in this function
align_needwunsQS.c:39: note: 'lkup_val' was declared here
align_needwunsQS.c:26: warning: 'sc' may be used uninitialized in this function
align_needwunsQS.c:26: note: 'sc' was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c align_utils.c -o align_utils.o
align_utils.c: In function 'PairwiseAlignmentsSingleSubject_align_aligned':
align_utils.c:223: warning: 'indelWidthSubject' may be used uninitialized in this function
align_utils.c:223: warning: 'indelStartSubject' may be used uninitialized in this function
align_utils.c:223: warning: 'indelWidthPattern' may be used uninitialized in this function
align_utils.c:223: warning: 'indelStartPattern' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c find_palindromes.c -o find_palindromes.o
find_palindromes.c: In function 'find_palindromes':
find_palindromes.c:26: warning: 'letter0' may be used uninitialized in this function
find_palindromes.c:26: note: 'letter0' was declared here
find_palindromes.c:25: warning: 'all_letter0' may be used uninitialized in this function
find_palindromes.c:25: note: 'all_letter0' was declared here
find_palindromes.c:82: warning: 'letter0' may be used uninitialized in this function
find_palindromes.c:82: note: 'letter0' was declared here
find_palindromes.c:81: warning: 'lkup_val' may be used uninitialized in this function
find_palindromes.c:81: note: 'lkup_val' was declared here
find_palindromes.c:81: warning: 'all_letter0' may be used uninitialized in this function
find_palindromes.c:81: note: 'all_letter0' was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c gtestsim.c -o gtestsim.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c inject_code.c -o inject_code.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c io_utils.c -o io_utils.o
io_utils.c: In function 'open_input_file':
io_utils.c:70: warning: unused variable 'buf'
io_utils.c:69: warning: unused variable 'ret'
io_utils.c: In function 'new_input_ExternalFilePtr':
io_utils.c:68: warning: 'fp' may be used uninitialized in this function
io_utils.c:68: note: 'fp' was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c letter_frequency.c -o letter_frequency.o
letter_frequency.c: In function 'XStringSet_two_way_letter_frequency':
letter_frequency.c:854: warning: unused variable 'x_pos'
letter_frequency.c:853: warning: unused variable 'ans_dimnames'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_BOC.c -o match_BOC.o
match_BOC.c: In function 'BOC_preprocess':
match_BOC.c:82: warning: overflow in implicit constant conversion
match_BOC.c: In function 'BOC_exact_search':
match_BOC.c:331: warning: label 'continue0' defined but not used
match_BOC.c:268: warning: unused variable 'noffsets'
match_BOC.c:268: warning: unused variable 'offsets'
match_BOC.c:268: warning: unused variable 'j'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_BOC2.c -o match_BOC2.o
match_BOC2.c: In function 'BOC2_exact_search':
match_BOC2.c:288: warning: label 'continue0' defined but not used
match_BOC2.c:234: warning: unused variable 'noffsets'
match_BOC2.c:234: warning: unused variable 'offsets'
match_BOC2.c:234: warning: unused variable 'j'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_PWM.c -o match_PWM.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_pattern.c -o match_pattern.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
match_pattern_boyermoore.c: In function '_match_pattern_boyermoore':
match_pattern_boyermoore.c:399: warning: '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
match_pattern_boyermoore.c:401: warning: 'c' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_pattern_indels.c -o match_pattern_indels.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_pdict.c -o match_pdict.o
match_pdict.c: In function 'init_vcount_collapsed_ans':
match_pdict.c:110: warning: 'ans_length' may be used uninitialized in this function
match_pdict.c: In function 'vmatch_XStringSet_XStringSet':
match_pdict.c:463: warning: 'ans_elt' may be used uninitialized in this function
match_pdict.c:463: note: 'ans_elt' was declared here
match_pdict.c: In function 'vmatch_PDict3Parts_XStringSet':
match_pdict.c:414: warning: 'ans_col' may be used uninitialized in this function
match_pdict.c:414: note: 'ans_col' was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c:641: warning: 'a_nice_max_nodeextbuf_nelt' defined but not used
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_pdict_Twobit.c -o match_pdict_Twobit.o
match_pdict_Twobit.c: In function 'build_Twobit':
match_pdict_Twobit.c:125: warning: 'twobit_sign2pos' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function 'match_ppheadtail0':
match_pdict_utils.c:664: warning: unused variable 'ncol'
match_pdict_utils.c: In function 'match_ppheadtail':
match_pdict_utils.c:722: warning: unused variable 'nelt'
match_pdict_utils.c: In function '_match_pdict_all_flanks':
match_pdict_utils.c:821: warning: unused variable 'subtotal_NFC'
match_pdict_utils.c:821: warning: unused variable 'total_NFC'
match_pdict_utils.c:820: warning: unused variable 'NFC'
match_pdict_utils.c:820: warning: unused variable 'nloci'
match_pdict_utils.c:820: warning: unused variable 'ndup'
match_pdict_utils.c: At top level:
match_pdict_utils.c:279: warning: 'match_headtail_by_loc' defined but not used
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_reporting.c -o match_reporting.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c matchprobes.c -o matchprobes.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c pmatchPattern.c -o pmatchPattern.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c replace_letter_at.c -o replace_letter_at.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c strutils.c -o strutils.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c translate.c -o translate.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c utils.c -o utils.o
utils.c: In function '_get_twobit_signature_at':
utils.c:210: warning: 'twobit_sign' may be used uninitialized in this function
utils.c: In function '_get_twobit_signature':
utils.c:196: warning: 'twobit_sign' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c xscat.c -o xscat.o
xscat.c: In function 'XStringSet_xscat':
xscat.c:94: warning: 'ans_length' is used uninitialized in this function
xscat.c:70: warning: 'ans_element_type' may be used uninitialized in this function
xscat.c: In function 'XString_xscat':
xscat.c:36: warning: 'ans_length' is used uninitialized in this function
xscat.c:18: warning: 'ans_classname' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o SparseList_utils.o XStringSet_class.o XStringSet_io.o XString_class.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o io_utils.o letter_frequency.o lowlevel_matching.o match_BOC.o match_BOC2.o match_PWM.o match_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-2.12-bioc/meat/Biostrings.Rcheck/Biostrings/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'setequal' from package 'base' in package 'Biostrings'
Creating a generic function for 'ls' from package 'base' in package 'Biostrings'
Creating a new generic function for 'offset' in package 'Biostrings'
** help
*** installing help indices
** building package indices
** installing vignettes
   'Biostrings2Classes.Rnw' 
   'BiostringsQuickOverview.Rnw' 
   'MultipleAlignments.Rnw' 
   'PairwiseAlignments.Rnw' 
   'matchprobes.Rnw' 
** testing if installed package can be loaded
* DONE (Biostrings)

name	user	system	elapsed
AAString-class	0.019	0.008	0.027
AMINO_ACID_CODE	0.135	0.009	0.143
AlignedXStringSet-class	0.161	0.026	0.187
DNAString-class	0.017	0.009	0.027
GENETIC_CODE	0.016	0.011	0.028
HNF4alpha	0.083	0.010	0.094
IUPAC_CODE_MAP	0.024	0.009	0.032
MIndex-class	0.010	0.008	0.018
MaskedXString-class	0.455	0.062	0.588
MultipleAlignment-class	3.313	0.069	3.384
PDict-class	7.970	0.545	8.570
PairwiseAlignments-class	0.630	0.073	0.713
PairwiseAlignments-io	3.511	0.720	4.311
QualityScaledXStringSet-class	0.052	0.012	0.064
RNAString-class	0.022	0.011	0.033
XString-class	0.032	0.026	0.058
XStringQuality-class	0.203	0.043	0.244
XStringSet-class	12.717	1.943	14.757
XStringSet-comparison	5.398	1.385	6.810
XStringSet-io	7.745	1.289	9.128
XStringSetList-class	0.418	0.055	0.476
XStringViews-class	0.453	0.062	0.515
align-utils	0.180	0.032	0.212
chartr	1.568	0.119	1.690
detail	1.399	0.045	1.456
dinucleotideFrequencyTest	0.023	0.015	0.039
findPalindromes	10.933	0.129	11.063
getSeq	0.133	0.053	0.186
gregexpr2	0.006	0.009	0.015
injectHardMask	0.088	0.028	0.118
letter	0.089	0.040	0.130
letterFrequency	2.127	0.469	2.608
longestConsecutive	0.003	0.005	0.008
lowlevel-matching	0.942	0.215	1.163
maskMotif	2.521	0.317	2.857
match-utils	0.067	0.012	0.079
matchLRPatterns	1.203	0.097	1.318
matchPDict-exact	371.104	5.881	377.197
matchPDict-inexact	63.138	2.173	65.421
matchPWM	5.336	0.095	5.433
matchPattern	5.316	0.253	5.577
matchProbePair	2.532	0.093	2.630
matchprobes	0.884	0.052	1.035
misc	0.045	0.016	0.062
needwunsQS	0.007	0.017	0.025
nucleotideFrequency	2.304	0.334	2.649
pairwiseAlignment	0.995	0.603	1.606
phiX174Phage	0.809	0.261	1.074
pid	0.482	0.336	0.830
replaceLetterAt	1.194	0.420	1.632
reverseComplement	3.754	0.906	4.681
stringDist	16.351	0.273	16.636
substitution_matrices	0.793	0.337	1.148
toComplex	0.010	0.016	0.026
translate	2.492	0.091	2.586
trimLRPatterns	0.322	0.033	0.354
xscat	3.825	0.427	4.278
yeastSEQCHR1	0.006	0.006	0.013

Summary

Command output