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BioC 2.13: CHECK report for Biostrings on perceval

This page was generated on 2014-04-05 09:51:39 -0700 (Sat, 05 Apr 2014).

Package 91/750HostnameOS / ArchBUILDCHECKBUILD BIN
Biostrings 2.30.1
H. Pages
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/Biostrings
Last Changed Rev: 83243 / Revision: 88450
Last Changed Date: 2013-11-12 19:15:35 -0800 (Tue, 12 Nov 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ WARNINGS ] OK 

Summary

Package: Biostrings
Version: 2.30.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biostrings_2.30.1.tar.gz
StartedAt: 2014-04-04 23:48:32 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-05 00:01:23 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 770.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Biostrings.Rcheck
Warnings: 1

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/Biostrings.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biostrings/DESCRIPTION’ ... OK
* this is package ‘Biostrings’ version ‘2.30.1’
* 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/26s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘BiocGenerics’ ‘IRanges’ ‘XVector’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Unexported objects imported by ‘:::’ calls:
  ‘IRanges:::.showAtomicList’ ‘IRanges:::extractROWS’
  ‘IRanges:::normalizeDoubleBracketSubscript’
  ‘IRanges:::showRangesList’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 ... OK
* 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 ... NOTE
File ‘/Users/biocbuild/bbs-2.13-bioc/meat/Biostrings.Rcheck/Biostrings/libs/Biostrings.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘align_pairwiseAlignment.o’
  Found ‘_putchar’, possibly from ‘putchar’ (C)
    Object: ‘align_pairwiseAlignment.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘Biostrings2Classes.Rnw’, ‘BiostringsQuickOverview.Rnw’,
  ‘matchprobes.Rnw’, ‘MultipleAlignments.Rnw’, ‘PairwiseAlignments.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [543s/554s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
matchPDict-exact      313.388  8.625 323.972
matchPDict-inexact     66.418  2.987  69.511
XStringSet-io          14.431  1.606  16.108
XStringSet-class       13.729  2.106  16.316
replaceAt               9.823  4.800  14.632
PDict-class            13.750  0.425  14.250
findPalindromes        12.237  0.727  13.033
stringDist              9.668  0.065   9.750
XStringSet-comparison   7.355  1.669   9.031
matchPattern            6.546  0.295  11.490
matchPWM                4.992  0.049   5.042
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 6 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/Biostrings.Rcheck/00check.log’
for details.

Biostrings.Rcheck/00install.out:

* installing *source* package ‘Biostrings’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c BAB_class.c -o BAB_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c BitMatrix.c -o BitMatrix.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c IRanges_stubs.c -o IRanges_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -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’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c PreprocessedTB_class.c -o PreprocessedTB_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c R_init_Biostrings.c -o R_init_Biostrings.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c RoSeqs_utils.c -o RoSeqs_utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c SparseList_utils.c -o SparseList_utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c XStringSet_class.c -o XStringSet_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c XStringSet_io.c -o XStringSet_io.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c XString_class.c -o XString_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c XVector_stubs.c -o XVector_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c align_needwunsQS.c -o align_needwunsQS.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c align_utils.c -o align_utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c find_palindromes.c -o find_palindromes.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c gtestsim.c -o gtestsim.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c inject_code.c -o inject_code.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -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’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c letter_frequency.c -o letter_frequency.o
letter_frequency.c: In function ‘XStringSet_two_way_letter_frequency’:
letter_frequency.c:957: warning: unused variable ‘x_pos’
letter_frequency.c:956: warning: unused variable ‘ans_dimnames’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c lowlevel_matching.c -o lowlevel_matching.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -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’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -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’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c match_PWM.c -o match_PWM.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c match_pattern.c -o match_pattern.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c match_pattern_indels.c -o match_pattern_indels.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c match_pattern_shiftor.c -o match_pattern_shiftor.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c match_pdict.c -o match_pdict.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c match_pdict_Twobit.c -o match_pdict_Twobit.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -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:665: warning: unused variable ‘ncol’
match_pdict_utils.c: In function ‘match_ppheadtail’:
match_pdict_utils.c:723: warning: unused variable ‘nelt’
match_pdict_utils.c: In function ‘_match_pdict_all_flanks’:
match_pdict_utils.c:823: warning: unused variable ‘subtotal_NFC’
match_pdict_utils.c:823: warning: unused variable ‘total_NFC’
match_pdict_utils.c:822: warning: unused variable ‘NFC’
match_pdict_utils.c:822: warning: unused variable ‘nloci’
match_pdict_utils.c:822: 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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c match_reporting.c -o match_reporting.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c matchprobes.c -o matchprobes.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c pmatchPattern.c -o pmatchPattern.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c replace_letter_at.c -o replace_letter_at.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c strutils.c -o strutils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c translate.c -o translate.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c utils.c -o utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c xscat.c -o xscat.o
llvm-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 -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 XVector_stubs.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-2.13-bioc/meat/Biostrings.Rcheck/Biostrings/libs
** 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
** testing if installed package can be loaded
* DONE (Biostrings)

Biostrings.Rcheck/Biostrings-Ex.timings:

nameusersystemelapsed
AAString-class0.0140.0030.016
AMINO_ACID_CODE0.0130.0020.016
AlignedXStringSet-class0.3700.0120.383
DNAString-class0.0110.0030.014
GENETIC_CODE0.0150.0020.016
HNF4alpha0.0340.0010.035
IUPAC_CODE_MAP0.0170.0010.017
MIndex-class0.0040.0000.005
MaskedXString-class0.3660.0220.390
MultipleAlignment-class3.1520.0483.211
PDict-class13.750 0.42514.250
PairwiseAlignments-class0.8700.1321.006
PairwiseAlignments-io3.5740.3893.989
QualityScaledXStringSet-class0.0290.0090.038
RNAString-class0.0190.0100.028
XString-class0.0320.0240.055
XStringQuality-class0.1520.0350.187
XStringSet-class13.729 2.10616.316
XStringSet-comparison7.3551.6699.031
XStringSet-io14.431 1.60616.108
XStringSetList-class0.9000.0540.954
XStringViews-class0.3160.0380.354
align-utils0.1500.0240.174
chartr0.8660.0810.950
detail1.4880.0551.547
dinucleotideFrequencyTest0.0260.0090.036
findPalindromes12.237 0.72713.033
getSeq0.1260.0130.140
gregexpr20.0040.0060.010
injectHardMask0.0740.0150.090
letter0.0300.0130.042
letterFrequency2.3100.6352.947
longestConsecutive0.0020.0050.007
lowlevel-matching0.9540.2111.165
maskMotif1.8900.2302.169
match-utils0.0490.0110.060
matchLRPatterns0.7270.0670.817
matchPDict-exact313.388 8.625323.972
matchPDict-inexact66.418 2.98769.511
matchPWM4.9920.0495.042
matchPattern 6.546 0.29511.490
matchProbePair1.5610.0801.653
matchprobes0.5050.0350.544
misc0.0220.0090.031
needwunsQS0.0040.0090.014
nucleotideFrequency1.2590.2721.572
padAndClip1.2710.4671.766
pairwiseAlignment1.0520.3751.450
phiX174Phage0.8220.0890.914
pid0.4060.0800.487
replaceAt 9.823 4.80014.632
replaceLetterAt1.1520.5631.723
reverseComplement2.4670.9803.460
stringDist9.6680.0659.750
substitution_matrices0.9470.1951.145
toComplex0.0060.0070.013
translate1.9320.0361.969
trimLRPatterns0.1300.0160.146
xscat2.8880.4903.382
yeastSEQCHR10.0050.0050.010