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BioC 2.14: CHECK report for Biostrings on petty

This page was generated on 2014-10-08 08:57:02 -0700 (Wed, 08 Oct 2014).

Package 98/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biostrings 2.32.1
H. Pages
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/Biostrings
Last Changed Rev: 92179 / Revision: 95116
Last Changed Date: 2014-07-03 18:14:24 -0700 (Thu, 03 Jul 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ WARNINGS ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: Biostrings
Version: 2.32.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biostrings_2.32.1.tar.gz
StartedAt: 2014-10-07 20:57:45 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 21:14:21 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 995.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Biostrings.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biostrings_2.32.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/Biostrings.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘2.32.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... [34s/42s] 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 'compare' and siglist 'vector,XStringSet'
  generic 'compare' and siglist 'Vector,XStringSet'
  generic 'compare' and siglist 'XStringSet,vector'
  generic 'compare' and siglist 'XStringSet,Vector'
  generic 'match' and siglist 'vector,XStringSet'
  generic 'match' and siglist 'Vector,XStringSet'
  generic 'match' and siglist 'XStringSet,vector'
  generic 'match' and siglist 'XStringSet,Vector'
  generic 'relistToClass' and siglist 'XString'
  generic 'relistToClass' and siglist 'XStringSet'
  generic 'splitAsListReturnedClass' and siglist 'XString'
  generic 'splitAsListReturnedClass' and siglist 'XStringSet'
  generic 'twoWayAlphabetFrequency' and siglist 'XString,XString'
  generic 'twoWayAlphabetFrequency' and siglist 'XString,XStringSet'
  generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XString'
  generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XStringSet'
  generic 'unstrsplit' and siglist 'XStringSet'
  generic 'unstrsplit' and siglist 'XStringSetList'
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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/Users/biocbuild/bbs-2.14-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 files in ‘vignettes’ ... OK
* checking examples ... [11m/12m] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
matchPDict-exact      445.262  6.970 460.176
matchPDict-inexact     66.078  1.563  68.857
stringDist             21.299  0.069  22.250
XStringSet-class       15.301  0.784  16.356
findPalindromes        13.656  0.421  14.175
replaceAt              11.391  2.005  14.102
PDict-class            10.164  0.248  10.660
matchPattern            9.816  0.346  10.269
XStringSet-io           7.773  0.780   8.815
matchPWM                8.194  0.044   8.577
XStringSet-comparison   5.710  0.811   6.600
PairwiseAlignments-io   5.102  0.242   5.567
* 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 4 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c XStringSetList_class.c -o XStringSetList_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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c io_utils.c -o io_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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c unstrsplit_methods.c -o unstrsplit_methods.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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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 XStringSetList_class.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 unstrsplit_methods.o utils.o xscat.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-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-class0.0130.0010.013
AMINO_ACID_CODE0.0050.0010.006
AlignedXStringSet-class0.3690.0050.375
DNAString-class0.0050.0000.006
GENETIC_CODE0.0260.0040.029
HNF4alpha0.0560.0020.065
IUPAC_CODE_MAP0.0170.0030.020
MIndex-class0.0020.0000.001
MaskedXString-class0.7410.0210.863
MultipleAlignment-class4.5490.0374.672
PDict-class10.164 0.24810.660
PairwiseAlignments-class0.4050.0420.502
PairwiseAlignments-io5.1020.2425.567
QualityScaledXStringSet-class0.0450.0010.046
RNAString-class0.0210.0010.022
XString-class0.0270.0010.030
XStringQuality-class0.2060.0020.209
XStringSet-class15.301 0.78416.356
XStringSet-comparison5.7100.8116.600
XStringSet-io7.7730.7808.815
XStringSetList-class1.2180.0161.237
XStringViews-class0.5830.0070.599
align-utils0.0900.0030.093
chartr1.3090.0741.406
detail2.3530.0732.468
dinucleotideFrequencyTest0.0260.0010.026
findPalindromes13.656 0.42114.175
getSeq0.2470.0140.261
gregexpr20.0040.0010.004
injectHardMask0.1200.0020.123
letter0.0420.0010.044
letterFrequency3.1920.3703.605
longestConsecutive0.0010.0000.002
lowlevel-matching1.2530.1221.400
maskMotif2.6260.1832.848
match-utils0.0690.0010.071
matchLRPatterns1.1790.0781.283
matchPDict-exact445.262 6.970460.176
matchPDict-inexact66.078 1.56368.857
matchPWM8.1940.0448.577
matchPattern 9.816 0.34610.269
matchProbePair2.4680.0612.630
matchprobes1.1910.0571.268
misc0.0310.0010.032
needwunsQS0.0020.0000.003
nucleotideFrequency1.8050.1362.030
padAndClip1.6670.1612.094
pairwiseAlignment1.6530.2061.942
phiX174Phage1.2240.0331.296
pid0.7490.0610.850
replaceAt11.391 2.00514.102
replaceLetterAt1.3880.3351.784
reverseComplement3.2250.3453.685
stringDist21.299 0.06922.250
substitution_matrices1.2250.1171.343
toComplex0.0060.0010.006
translate3.2170.0263.251
trimLRPatterns0.2250.0030.285
xscat3.7790.1543.954
yeastSEQCHR10.0070.0000.008