BioC 3.2: CHECK report for Biostrings on perceval

Package: Biostrings

Version: 2.38.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Biostrings_2.38.0.tar.gz

StartedAt: 2015-11-10 02:36:00 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 02:48:57 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 777.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Biostrings.Rcheck

Warnings: 2

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Biostrings_2.38.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Biostrings.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘2.38.0’
* 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 ... [20s/21s] OK
* checking installed package size ... NOTE
  installed size is 14.2Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata  11.1Mb
* 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.
Versioned 'LinkingTo' value for ‘S4Vectors’ is only usable in R >= 3.0.2
* 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:
  ‘BiocGenerics:::testPackage’ ‘IRanges:::.showAtomicList’
  ‘IRanges:::showRangesList’ ‘S4Vectors:::anyMissingOrOutside’
  ‘S4Vectors:::duplicatedIntegerPairs’
  See the note in ?`:::` about the use of this operator.
* 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 'translate.Rd':
  ‘[GenomicFeatures]{extractTranscriptsFromGenome}’

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

* 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 '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 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 compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11m/11m] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
matchPDict-exact   418.329  4.827 423.176
matchPDict-inexact  54.149  0.935  55.086
findPalindromes     44.652  0.560  45.482
XStringSet-io       18.235  0.553  19.000
matchPattern        16.622  0.334  16.956
XStringSet-class    12.083  0.490  12.735
stringDist          10.922  0.020  10.948
replaceAt            5.380  1.080   6.460
matchPWM             5.456  0.009   5.466
PDict-class          4.874  0.145   5.089
* 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
* DONE

Status: 2 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/Biostrings.Rcheck/00check.log’
for details.

* 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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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:193: 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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c S4Vectors_stubs.c -o S4Vectors_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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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:674: warning: unused variable ‘ncol’
match_pdict_utils.c: In function ‘match_ppheadtail’:
match_pdict_utils.c:734: warning: unused variable ‘nelt’
match_pdict_utils.c: In function ‘_match_pdict_all_flanks’:
match_pdict_utils.c:841: warning: unused variable ‘subtotal_NFC’
match_pdict_utils.c:841: warning: unused variable ‘total_NFC’
match_pdict_utils.c:840: warning: unused variable ‘NFC’
match_pdict_utils.c:840: warning: unused variable ‘nloci’
match_pdict_utils.c:840: warning: unused variable ‘ndup’
match_pdict_utils.c: At top level:
match_pdict_utils.c:287: 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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/Library/Frameworks/R.framework/Resources/lib -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 S4Vectors_stubs.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 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-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)

name	user	system	elapsed
AAString-class	0.006	0.000	0.006
AMINO_ACID_CODE	0.003	0.000	0.003
AlignedXStringSet-class	0.079	0.012	0.090
DNAString-class	0.003	0.001	0.003
GENETIC_CODE	0.015	0.004	0.019
HNF4alpha	0.027	0.003	0.031
IUPAC_CODE_MAP	0.006	0.000	0.007
MIndex-class	0.000	0.001	0.001
MaskedXString-class	0.266	0.007	0.307
MultipleAlignment-class	1.556	0.016	1.572
PDict-class	4.874	0.145	5.089
PairwiseAlignments-class	0.181	0.013	0.194
PairwiseAlignments-io	2.838	0.172	3.010
QualityScaledXStringSet-class	0.018	0.000	0.019
RNAString-class	0.01	0.00	0.01
XString-class	0.013	0.001	0.013
XStringQuality-class	0.070	0.002	0.070
XStringSet-class	12.083	0.490	12.735
XStringSet-comparison	3.333	0.460	3.793
XStringSet-io	18.235	0.553	19.000
XStringSetList-class	0.429	0.040	0.467
XStringViews-class	0.165	0.032	0.197
align-utils	0.100	0.013	0.124
chartr	1.034	0.045	1.107
detail	0.979	0.039	1.018
dinucleotideFrequencyTest	0.015	0.001	0.016
findPalindromes	44.652	0.560	45.482
getSeq	0.222	0.004	0.224
gregexpr2	0.002	0.000	0.002
injectHardMask	0.047	0.001	0.047
letter	0.017	0.000	0.017
letterFrequency	2.037	0.210	2.247
longestConsecutive	0.001	0.000	0.001
lowlevel-matching	0.742	0.103	0.845
maskMotif	1.535	0.135	1.669
match-utils	0.027	0.001	0.028
matchLRPatterns	0.985	0.053	1.101
matchPDict-exact	418.329	4.827	423.176
matchPDict-inexact	54.149	0.935	55.086
matchPWM	5.456	0.009	5.466
matchPattern	16.622	0.334	16.956
matchProbePair	1.942	0.050	1.992
matchprobes	0.462	0.008	0.469
misc	0.017	0.001	0.017
needwunsQS	0.001	0.000	0.001
nucleotideFrequency	1.23	0.06	1.29
padAndClip	0.829	0.080	0.909
pairwiseAlignment	0.859	0.102	0.961
phiX174Phage	0.671	0.069	0.741
pid	0.341	0.050	0.391
replaceAt	5.38	1.08	6.46
replaceLetterAt	0.802	0.122	0.924
reverseComplement	2.055	0.282	2.336
stringDist	10.922	0.020	10.948
substitution_matrices	0.521	0.018	0.539
toComplex	0.003	0.001	0.003
translate	1.002	0.036	1.038
trimLRPatterns	0.134	0.001	0.135
xscat	1.610	0.082	1.691
yeastSEQCHR1	0.005	0.001	0.005