Biostrings

Package: Biostrings
Title: String objects representing biological sequences, and matching
algorithms
Description: Memory efficient string containers, string matching
algorithms, and other utilities, for fast manipulation of large
biological sequences or sets of sequences.
Version: 2.40.2
Encoding: UTF-8
Author: H. Pagès, P. Aboyoun, R. Gentleman, and S. DebRoy
Maintainer: H. Pagès <hpages@fredhutch.org>
biocViews: SequenceMatching, Alignment, Sequencing, Genetics,
DataImport, DataRepresentation, Infrastructure
Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.15.6), S4Vectors (>=
0.10.1), IRanges (>= 2.5.27), XVector (>= 0.11.6)
Imports: graphics, methods, stats, utils, BiocGenerics, IRanges,
XVector
LinkingTo: S4Vectors, IRanges, XVector
Enhances: Rmpi
Suggests: BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>=
1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11),
BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe,
hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy
(>= 1.41.3), affydata (>= 1.11.5), RUnit
License: Artistic-2.0
LazyLoad: yes
Collate: 00datacache.R utils.R IUPAC_CODE_MAP.R AMINO_ACID_CODE.R
GENETIC_CODE.R XStringCodec-class.R seqtype.R XString-class.R
XStringSet-class.R XStringSet-comparison.R XStringViews-class.R
MaskedXString-class.R XStringSetList-class.R xscat.R
XStringSet-io.R letter.R getSeq.R dinucleotideFrequencyTest.R
chartr.R reverseComplement.R translate.R toComplex.R
replaceAt.R replaceLetterAt.R injectHardMask.R padAndClip.R
unstrsplit-methods.R misc.R SparseList-class.R MIndex-class.R
lowlevel-matching.R match-utils.R matchPattern.R maskMotif.R
matchPattern.BOC.R matchPattern.BOC2.R matchLRPatterns.R
trimLRPatterns.R matchProbePair.R matchPWM.R findPalindromes.R
PDict-class.R matchPDict.R XStringPartialMatches-class.R
XStringQuality-class.R QualityScaledXStringSet.R
letterFrequency.R InDel-class.R AlignedXStringSet-class.R
PairwiseAlignments-class.R
PairwiseAlignmentsSingleSubject-class.R PairwiseAlignments-io.R
align-utils.R pmatchPattern.R pairwiseAlignment.R stringDist.R
needwunsQS.R MultipleAlignment.R matchprobes.R zzz.R
NeedsCompilation: yes
Packaged: 2016-06-08 01:29:00 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'Biostrings' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c BAB_class.c -o BAB_class.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c BitMatrix.c -o BitMatrix.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c MIndex_class.c -o MIndex_class.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c SparseList_utils.c -o SparseList_utils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c XStringSetList_class.c -o XStringSetList_class.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c XStringSet_class.c -o XStringSet_class.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c XStringSet_io.c -o XStringSet_io.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c XString_class.c -o XString_class.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c XVector_stubs.c -o XVector_stubs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c align_needwunsQS.c -o align_needwunsQS.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c align_utils.c -o align_utils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c find_palindromes.c -o find_palindromes.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c gtestsim.c -o gtestsim.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c inject_code.c -o inject_code.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c letter_frequency.c -o letter_frequency.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c lowlevel_matching.c -o lowlevel_matching.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c match_BOC.c -o match_BOC.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c match_BOC2.c -o match_BOC2.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c match_PWM.c -o match_PWM.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c match_pattern.c -o match_pattern.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c match_pattern_indels.c -o match_pattern_indels.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c match_pdict.c -o match_pdict.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c match_pdict_Twobit.c -o match_pdict_Twobit.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c match_pdict_utils.c -o match_pdict_utils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c match_reporting.c -o match_reporting.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c matchprobes.c -o matchprobes.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c pmatchPattern.c -o pmatchPattern.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c replaceAt.c -o replaceAt.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c replace_letter_at.c -o replace_letter_at.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c strutils.c -o strutils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c translate.c -o translate.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c utils.c -o utils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c xscat.c -o xscat.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -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 replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/Biostrings/libs
** R
** data
** inst
** preparing package for lazy loading
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
  converting help for package 'Biostrings'
    finding HTML links ... done
    AAString-class                          html  
    AMINO_ACID_CODE                         html  
    AlignedXStringSet-class                 html  
    BOC_SubjectString-class                 html  
    Biostrings-internals                    html  
    DNAString-class                         html  
    GENETIC_CODE                            html  
    HNF4alpha                               html  
    IUPAC_CODE_MAP                          html  
    InDel-class                             html  
    MIndex-class                            html  
    MaskedXString-class                     html  
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/MaskedXString-class.Rd:182: missing file link 'Views'
    MultipleAlignment-class                 html  
    finding level-2 HTML links ... done

Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/MultipleAlignment-class.Rd:124: missing file link 'narrow'
    PDict-class                             html  
    PairwiseAlignments-class                html  
    PairwiseAlignments-io                   html  
    QualityScaledXStringSet-class           html  
    RNAString-class                         html  
    XString-class                           html  
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/XString-class.Rd:180: missing file link 'subseq'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/XString-class.Rd:188: missing file link 'compact'
    XStringPartialMatches-class             html  
    XStringQuality-class                    html  
    XStringSet-class                        html  
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/XStringSet-class.Rd:90: missing file link 'narrow'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/XStringSet-class.Rd:177: missing file link 'subseq'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/XStringSet-class.Rd:197: missing file link 'IRanges'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/XStringSet-class.Rd:199: missing file link 'XVector'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/XStringSet-class.Rd:205: missing file link 'IRanges'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/XStringSet-class.Rd:211: missing file link 'threebands'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/XStringSet-class.Rd:216: missing file link 'subseq<-'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/XStringSet-class.Rd:217: missing file link 'XVector'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/XStringSet-class.Rd:218: missing file link 'subseq<-'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/XStringSet-class.Rd:316: missing file link 'subseq'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/XStringSet-class.Rd:317: missing file link 'narrow'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/XStringSet-class.Rd:319: missing file link 'compact'
    XStringSet-comparison                   html  
    XStringSet-io                           html  
    XStringSetList-class                    html  
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/XStringSetList-class.Rd:70: missing file link 'List'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/XStringSetList-class.Rd:77: missing file link 'elementNROWS'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/XStringSetList-class.Rd:78: missing file link 'PartitioningByEnd'
    XStringViews-class                      html  
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/XStringViews-class.Rd:155: missing file link 'gaps'
    align-utils                             html  
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/align-utils.Rd:87: missing file link 'coverage'
    chartr                                  html  
    detail                                  html  
    dinucleotideFrequencyTest               html  
    findPalindromes                         html  
    getSeq                                  html  
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/getSeq.Rd:9: missing file link 'BSgenome'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/getSeq.Rd:19: missing file link 'BSgenome'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/getSeq.Rd:33: missing file link 'getSeq,BSgenome-method'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/getSeq.Rd:34: missing file link 'BSgenome'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/getSeq.Rd:39: missing file link 'getSeq,BSgenome-method'
    gregexpr2                               html  
    injectHardMask                          html  
    letter                                  html  
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/letter.Rd:49: missing file link 'subseq'
    letterFrequency                         html  
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/letterFrequency.Rd:290: missing file link 'coverage'
    longestConsecutive                      html  
    lowlevel-matching                       html  
    maskMotif                               html  
    match-utils                             html  
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/match-utils.Rd:42: missing file link 'coverage'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/match-utils.Rd:48: missing file link 'coverage'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/match-utils.Rd:72: missing file link 'Rle'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/match-utils.Rd:74: missing file link 'coverage'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/match-utils.Rd:87: missing file link 'coverage'
    matchLRPatterns                         html  
    matchPDict-exact                        html  
    matchPDict-inexact                      html  
    matchPWM                                html  
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/matchPWM.Rd:84: missing file link 'Views'
    matchPattern                            html  
    matchProbePair                          html  
    matchprobes                             html  
    misc                                    html  
    needwunsQS                              html  
    nucleotideFrequency                     html  
    padAndClip                              html  
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/padAndClip.Rd:33: missing file link 'Ranges'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/padAndClip.Rd:108: missing file link 'Ranges'
    pairwiseAlignment                       html  
    phiX174Phage                            html  
    pid                                     html  
    pmatchPattern                           html  
    replaceAt                               html  
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/replaceAt.Rd:36: missing file link 'Ranges'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/replaceAt.Rd:37: missing file link 'RangesList'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/replaceAt.Rd:43: missing file link 'IntegerList'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/replaceAt.Rd:51: missing file link 'Ranges'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/replaceAt.Rd:52: missing file link 'RangesList'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/replaceAt.Rd:53: missing file link 'RangesList'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/replaceAt.Rd:72: missing file link 'CharacterList'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/replaceAt.Rd:98: missing file link 'subseq'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/replaceAt.Rd:103: missing file link 'Ranges'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/replaceAt.Rd:110: missing file link 'subseq'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/replaceAt.Rd:110: missing file link 'subseq<-'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/replaceAt.Rd:115: missing file link 'unstrsplit'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/replaceAt.Rd:127: missing file link 'Ranges'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/replaceAt.Rd:127: missing file link 'RangesList'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/replaceAt.Rd:128: missing file link 'IntegerList'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/replaceAt.Rd:128: missing file link 'CharacterList'
    replaceLetterAt                         html  
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/replaceLetterAt.Rd:43: missing file link 'Rle'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/replaceLetterAt.Rd:130: missing file link 'BSgenome'
    reverseComplement                       html  
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/reverseComplement.Rd:48: missing file link 'reverse'
Rd warning: /tmp/Rtmp3PBy8G/R.INSTALL5d5b63b892b1/Biostrings/man/reverseComplement.Rd:71: missing file link 'reverse'
    stringDist                              html  
    substitution_matrices                   html  
    toComplex                               html  
    translate                               html  
    trimLRPatterns                          html  
    xscat                                   html  
    yeastSEQCHR1                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Biostrings)
Making 'packages.html' ... done