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Last data update: 2014.03.03

IRanges

Package: IRanges
Title: Infrastructure for manipulating intervals on sequences
Description: The package provides efficient low-level and highly reusable S4
classes for storing ranges of integers, RLE vectors (Run-Length
Encoding), and, more generally, data that can be organized
sequentially (formally defined as Vector objects), as well as views
on these Vector objects.
Efficient list-like classes are also provided for storing big
collections of instances of the basic classes. All classes in
the package use consistent naming and share the same rich and
consistent "Vector API" as much as possible.
Version: 2.6.1
Encoding: UTF-8
Author: H. PagÃ¨s, P. Aboyoun and M. Lawrence
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
biocViews: Infrastructure, DataRepresentation
Depends: R (>= 3.1.0), methods, utils, stats, BiocGenerics (>=
0.15.10), S4Vectors (>= 0.9.48)
Imports: stats4
LinkingTo: S4Vectors
Suggests: XVector, GenomicRanges, GenomicFeatures, GenomicAlignments,
BSgenome.Celegans.UCSC.ce2, RUnit
License: Artistic-2.0
Collate: Vector-class-leftovers.R List-class-leftovers.R
AtomicList-class.R Ranges-class.R Ranges-comparison.R
IRanges-class.R IRanges-constructor.R IRanges-utils.R
Views-class.R Grouping-class.R CompressedList-class.R
CompressedList-comparison.R Rle-class-leftovers.R
RleViews-class.R RleViews-utils.R extractList.R seqapply.R
multisplit.R AtomicList-impl.R AtomicList-utils.R
ListGrouping-class.R Hits-class-leftovers.R DataFrame-utils.R
DataFrameList-class.R DataFrameList-utils.R RangesList-class.R
GappedRanges-class.R ViewsList-class.R RleViewsList-class.R
RleViewsList-utils.R MaskCollection-class.R RangedData-class.R
RDApplyParams-class.R RangedData-utils.R
CompressedHitsList-class.R NCList-class.R
RangedSelection-class.R read.Mask.R findOverlaps-methods.R
intra-range-methods.R inter-range-methods.R reverse-methods.R
coverage-methods.R slice-methods.R setops-methods.R
nearest-methods.R cbind-Rle-methods.R tile-methods.R
subsetting-internals.R zzz.R
NeedsCompilation: yes
Packaged: 2016-06-19 01:29:43 UTC; biocbuild

● BiocViews: DataRepresentation, Infrastructure
● 0 images, 43 functions, 0 datasets
● Reverse Depends: 241

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'IRanges' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c CompressedList_class.c -o CompressedList_class.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c GappedRanges_class.c -o GappedRanges_class.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c Grouping_class.c -o Grouping_class.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c IRanges_class.c -o IRanges_class.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c IRanges_constructor.c -o IRanges_constructor.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c NCList.c -o NCList.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c R_init_IRanges.c -o R_init_IRanges.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c Ranges_class.c -o Ranges_class.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c Ranges_comparison.c -o Ranges_comparison.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c RleViews_utils.c -o RleViews_utils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/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"   -fpic  -g -O2  -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c coverage_methods.c -o coverage_methods.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c inter_range_methods.c -o inter_range_methods.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o GappedRanges_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o Ranges_comparison.o RleViews_utils.o S4Vectors_stubs.o SimpleRangesList_class.o coverage_methods.o inter_range_methods.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/IRanges/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'window<-' from package 'stats' in package 'IRanges'
Creating a generic function for 'rev' from package 'base' in package 'IRanges'
Creating a generic function for 'stack' from package 'utils' in package 'IRanges'
Creating a generic function for 'mean' from package 'base' in package 'IRanges'
Creating a generic function for 'which.max' from package 'base' in package 'IRanges'
Creating a generic function for 'which.min' from package 'base' in package 'IRanges'
Creating a generic function for 'split<-' from package 'base' in package 'IRanges'
Creating a generic function for 'drop' from package 'base' in package 'IRanges'
Creating a generic function for 'which' from package 'base' in package 'IRanges'
Creating a generic function for 'diff' from package 'base' in package 'IRanges'
Creating a generic function for 'median' from package 'stats' in package 'IRanges'
Creating a generic function for 'quantile' from package 'stats' in package 'IRanges'
Creating a generic function for 'smoothEnds' from package 'stats' in package 'IRanges'
Creating a generic function for 'runmed' from package 'stats' in package 'IRanges'
Creating a generic function for 'chartr' from package 'base' in package 'IRanges'
Creating a generic function for 'tolower' from package 'base' in package 'IRanges'
Creating a generic function for 'toupper' from package 'base' in package 'IRanges'
Creating a generic function for 'sub' from package 'base' in package 'IRanges'
Creating a generic function for 'gsub' from package 'base' in package 'IRanges'
** help
*** installing help indices
  converting help for package 'IRanges'
    finding HTML links ... done
    AtomicList-class                        html  
    finding level-2 HTML links ... done

Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/AtomicList-class.Rd:291: missing file link 'List'
    AtomicList-utils                        html  
    CompressedHitsList-class                html  
    CompressedList-class                    html  
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/CompressedList-class.Rd:38: missing file link 'SimpleList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/CompressedList-class.Rd:39: missing file link 'List'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/CompressedList-class.Rd:44: missing file link 'SimpleList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/CompressedList-class.Rd:49: missing file link 'GRangesList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/CompressedList-class.Rd:50: missing file link 'GAlignmentsList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/CompressedList-class.Rd:60: missing file link 'SimpleList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/CompressedList-class.Rd:66: missing file link 'SimpleList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/CompressedList-class.Rd:81: missing file link 'List'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/CompressedList-class.Rd:84: missing file link 'SimpleList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/CompressedList-class.Rd:87: missing file link 'List'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/CompressedList-class.Rd:89: missing file link 'SimpleList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/CompressedList-class.Rd:95: missing file link 'List'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/CompressedList-class.Rd:100: missing file link 'List'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/CompressedList-class.Rd:105: missing file link 'List'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/CompressedList-class.Rd:110: missing file link 'List'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/CompressedList-class.Rd:118: missing file link 'classNameForDisplay'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/CompressedList-class.Rd:124: missing file link 'List'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/CompressedList-class.Rd:127: missing file link 'SimpleList'
    DataFrame-utils                         html  
    DataFrameList-class                     html  
    GappedRanges-class                      html  
    Grouping-class                          html  
    Hits-class-leftovers                    html  
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/Hits-class-leftovers.Rd:27: missing file link 'Hits'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/Hits-class-leftovers.Rd:57: missing file link 'Hits'
    IRanges-class                           html  
    IRanges-constructor                     html  
    IRanges-internals                       html  
    IRanges-utils                           html  
    IRangesList-class                       html  
    List-class-leftovers                    html  
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/List-class-leftovers.Rd:11: missing file link 'List'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/List-class-leftovers.Rd:35: missing file link 'List'
    MaskCollection-class                    html  
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/MaskCollection-class.Rd:206: missing file link 'alphabetFrequency'
    NCList-class                            html  
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/NCList-class.Rd:79: missing file link 'GNCList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/NCList-class.Rd:99: missing file link 'GNCList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/NCList-class.Rd:100: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/NCList-class.Rd:108: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/NCList-class.Rd:123: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/NCList-class.Rd:125: missing file link 'GNCList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/NCList-class.Rd:128: missing file link 'GNCList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/NCList-class.Rd:152: missing file link 'GNCList'
    RDApplyParams-class                     html  
    RangedData-class                        html  
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/RangedData-class.Rd:78: missing file link 'GRangesList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/RangedData-class.Rd:79: missing file link 'GRangesList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/RangedData-class.Rd:82: missing file link 'GRanges'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/RangedData-class.Rd:83: missing file link 'GRangesList'
    RangedDataList-class                    html  
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/RangedDataList-class.Rd:13: missing file link 'GRangesList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/RangedDataList-class.Rd:14: missing file link 'GRangesList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/RangedDataList-class.Rd:17: missing file link 'GRanges'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/RangedDataList-class.Rd:18: missing file link 'GRangesList'
    RangedSelection-class                   html  
    Ranges-class                            html  
    Ranges-comparison                       html  
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/Ranges-comparison.Rd:136: missing file link 'GenomicRanges'
    RangesList-class                        html  
    Rle-class-leftovers                     html  
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/Rle-class-leftovers.Rd:22: missing file link 'Rle'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/Rle-class-leftovers.Rd:71: missing file link 'Rle'
    RleViews-class                          html  
    RleViewsList-class                      html  
    Vector-class-leftovers                  html  
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/Vector-class-leftovers.Rd:36: missing file link 'Vector'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/Vector-class-leftovers.Rd:161: missing file link 'Vector'
    Views-class                             html  
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/Views-class.Rd:46: missing file link 'XIntegerViews'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/Views-class.Rd:47: missing file link 'XStringViews'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/Views-class.Rd:156: missing file link 'XVector'
    ViewsList-class                         html  
    coverage-methods                        html  
    extractList                             html  
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/extractList.Rd:26: missing file link 'split'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/extractList.Rd:97: missing file link 'relistToClass'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/extractList.Rd:151: missing file link 'relistToClass'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/extractList.Rd:162: missing file link 'unsplit'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/extractList.Rd:165: missing file link 'split'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/extractList.Rd:168: missing file link 'Vector'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/extractList.Rd:168: missing file link 'List'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/extractList.Rd:169: missing file link 'Rle'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/extractList.Rd:169: missing file link 'DataFrame'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/extractList.Rd:171: missing file link 'relistToClass'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/extractList.Rd:172: missing file link 'List'
    findOverlaps-methods                    html  
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/findOverlaps-methods.Rd:72: missing file link 'findOverlaps,GenomicRanges,GenomicRanges-method'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/findOverlaps-methods.Rd:74: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/findOverlaps-methods.Rd:74: missing file link 'GRangesList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/findOverlaps-methods.Rd:159: missing file link 'Hits'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/findOverlaps-methods.Rd:168: missing file link 'HitsList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/findOverlaps-methods.Rd:190: missing file link 'Hits'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/findOverlaps-methods.Rd:190: missing file link 'HitsList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/findOverlaps-methods.Rd:243: missing file link 'Hits'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/findOverlaps-methods.Rd:243: missing file link 'HitsList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/findOverlaps-methods.Rd:251: missing file link 'Hits'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/findOverlaps-methods.Rd:252: missing file link 'HitsList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/findOverlaps-methods.Rd:265: missing file link 'Hits'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/findOverlaps-methods.Rd:265: missing file link 'HitsList'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/findOverlaps-methods.Rd:269: missing file link 'findOverlaps,GenomicRanges,GenomicRanges-method'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/findOverlaps-methods.Rd:271: missing file link 'GRanges'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/findOverlaps-methods.Rd:271: missing file link 'GRangesList'
    inter-range-methods                     html  
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/inter-range-methods.Rd:265: missing file link 'endoapply'
    intra-range-methods                     html  
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/intra-range-methods.Rd:280: missing file link 'GRanges'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/intra-range-methods.Rd:281: missing file link 'promoters,GenomicRanges-method'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/intra-range-methods.Rd:336: missing file link 'endoapply'
    multisplit                              html  
    nearest-methods                         html  
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/nearest-methods.Rd:159: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/nearest-methods.Rd:160: missing file link 'GRanges'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/nearest-methods.Rd:173: missing file link 'precede,GenomicRanges,GenomicRanges-method'
    read.Mask                               html  
    reverse-methods                         html  
    seqapply                                html  
    setops-methods                          html  
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/setops-methods.Rd:84: missing file link 'Pairs'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/setops-methods.Rd:109: missing file link 'Pairs'
Rd warning: /tmp/RtmpdBBMpY/R.INSTALL5a965ad36c91/IRanges/man/setops-methods.Rd:148: missing file link 'mendoapply'
    slice-methods                           html  
    view-summarization-methods              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (IRanges)
Making 'packages.html' ... done