S4Vectors

Package: S4Vectors
Title: S4 implementation of vectors and lists
Description: The S4Vectors package defines the Vector and List virtual classes
and a set of generic functions that extend the semantic of ordinary
vectors and lists in R. Package developers can easily implement
vector-like or list-like objects as concrete subclasses of Vector or
List. In addition, a few low-level concrete subclasses of general
interest (e.g. DataFrame, Rle, and Hits) are implemented in the
S4Vectors package itself (many more are implemented in the IRanges
package and in other Bioconductor infrastructure packages).
Version: 0.10.1
Encoding: UTF-8
Author: H. Pagès, M. Lawrence and P. Aboyoun
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
biocViews: Infrastructure, DataRepresentation
Depends: R (>= 3.3.0), methods, utils, stats, stats4, BiocGenerics (>=
0.15.10)
Suggests: IRanges, GenomicRanges, RUnit
License: Artistic-2.0
Collate: S4-utils.R show-utils.R utils.R normarg-utils.R isSorted.R
subsetting-utils.R vector-utils.R logical-utils.R int-utils.R
str-utils.R eval-utils.R DataTable-class.R Annotated-class.R
Vector-class.R Vector-comparison.R Vector-setops.R Hits-class.R
Hits-comparison.R Hits-setops.R Rle-class.R Rle-utils.R
List-class.R List-comparison.R List-utils.R SimpleList-class.R
HitsList-class.R DataFrame-class.R expand-methods.R
FilterRules-class.R aggregate-methods.R shiftApply-methods.R
split-methods.R Pairs-class.R zzz.R
NeedsCompilation: yes
Packaged: 2016-05-22 04:29:51 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'S4Vectors' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c AEbufs.c -o AEbufs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c DataFrame_class.c -o DataFrame_class.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Hits_class.c -o Hits_class.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c List_class.c -o List_class.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Rle_class.c -o Rle_class.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Rle_utils.c -o Rle_utils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c SEXP_utils.c -o SEXP_utils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c SimpleList_class.c -o SimpleList_class.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c anyMissing.c -o anyMissing.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c eval_utils.c -o eval_utils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c hash_utils.c -o hash_utils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c int_utils.c -o int_utils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c logical_utils.c -o logical_utils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c safe_arithm.c -o safe_arithm.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c sort_utils.c -o sort_utils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c str_utils.c -o str_utils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c vector_utils.c -o vector_utils.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o eval_utils.o hash_utils.o int_utils.o logical_utils.o safe_arithm.o sort_utils.o str_utils.o vector_utils.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/S4Vectors/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'head' from package 'utils' in package 'S4Vectors'
Creating a generic function for 'tail' from package 'utils' in package 'S4Vectors'
Creating a generic function for 'na.omit' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'na.exclude' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'complete.cases' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'transform' from package 'base' in package 'S4Vectors'
Creating a generic function for 'merge' from package 'base' in package 'S4Vectors'
Creating a new generic function for 'rowSums' in package 'S4Vectors'
Creating a new generic function for 'colSums' in package 'S4Vectors'
Creating a new generic function for 'rowMeans' in package 'S4Vectors'
Creating a new generic function for 'colMeans' in package 'S4Vectors'
Creating a generic function for 'as.matrix' from package 'base' in package 'S4Vectors'
Creating a generic function for 'window' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'with' from package 'base' in package 'S4Vectors'
Creating a new generic function for 'expand.grid' in package 'S4Vectors'
Creating a generic function for 'by' from package 'base' in package 'S4Vectors'
Creating a generic function for '%in%' from package 'base' in package 'S4Vectors'
Creating a new generic function for 'findMatches' in package 'S4Vectors'
Creating a generic function for 'setequal' from package 'base' in package 'S4Vectors'
Creating a generic function for 'as.table' from package 'base' in package 'S4Vectors'
Creating a generic function for 't' from package 'base' in package 'S4Vectors'
Creating a generic function for 'as.factor' from package 'base' in package 'S4Vectors'
Creating a generic function for 'rev' from package 'base' in package 'S4Vectors'
Creating a generic function for 'which' from package 'base' in package 'S4Vectors'
Creating a generic function for 'which.max' from package 'base' in package 'S4Vectors'
Creating a generic function for 'ifelse' from package 'base' in package 'S4Vectors'
Creating a generic function for 'diff' from package 'base' in package 'S4Vectors'
Creating a generic function for 'mean' from package 'base' in package 'S4Vectors'
Creating a generic function for 'var' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'cov' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'cor' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'sd' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'median' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'smoothEnds' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'runmed' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Creating a generic function for 'substr' from package 'base' in package 'S4Vectors'
Creating a generic function for 'substring' from package 'base' in package 'S4Vectors'
Creating a generic function for 'chartr' from package 'base' in package 'S4Vectors'
Creating a generic function for 'tolower' from package 'base' in package 'S4Vectors'
Creating a generic function for 'toupper' from package 'base' in package 'S4Vectors'
Creating a generic function for 'sub' from package 'base' in package 'S4Vectors'
Creating a generic function for 'gsub' from package 'base' in package 'S4Vectors'
Creating a generic function for 'levels' from package 'base' in package 'S4Vectors'
Creating a generic function for 'droplevels' from package 'base' in package 'S4Vectors'
in method for 'unique' with signature '"SimpleList"': no definition for class "SimpleList"
Creating a generic function for 'within' from package 'base' in package 'S4Vectors'
Creating a generic function for 'aggregate' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'split' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
  converting help for package 'S4Vectors'
    finding HTML links ... done
    Annotated-class                         html  
    DataFrame-class                         html  
    DataTable-class                         html  
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/DataTable-class.Rd:52: missing file link 'RangedData'
    FilterMatrix-class                      html  
    FilterRules-class                       html  
    Hits-class                              html  
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/Hits-class.Rd:80: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/Hits-class.Rd:246: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/Hits-class.Rd:249: missing file link 'Hits-examples'
    Hits-comparison                         html  
    Hits-setops                             html  
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/Hits-setops.Rd:47: missing file link 'union'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/Hits-setops.Rd:48: missing file link 'intersect'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/Hits-setops.Rd:49: missing file link 'setdiff'
    HitsList-class                          html  
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/HitsList-class.Rd:37: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/HitsList-class.Rd:38: missing file link 'RangesList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/HitsList-class.Rd:47: missing file link 'RangesList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/HitsList-class.Rd:70: missing file link 'RangesList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/HitsList-class.Rd:101: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/HitsList-class.Rd:103: missing file link 'RangesList'
    List-class                              html  
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:59: missing file link 'IntegerList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:73: missing file link 'IntegerList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:73: missing file link 'RleList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:74: missing file link 'RangesList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:75: missing file link 'GRangesList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:79: missing file link 'GRangesList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:83: missing file link 'IntegerList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:84: missing file link 'RleList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:84: missing file link 'RangesList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:94: missing file link 'CompressedList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:148: missing file link 'CompressedList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:156: missing file link 'CompressedList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:219: missing file link 'IntegerList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:220: missing file link 'LogicalList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:220: missing file link 'CharacterList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:221: missing file link 'RleList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:222: missing file link 'RleList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:222: missing file link 'RangesList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:272: missing file link 'CompressedList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:275: missing file link 'IntegerList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:275: missing file link 'RleList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-class.Rd:276: missing file link 'IRanges'
    List-utils                              html  
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-utils.Rd:95: missing file link 'sapply'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-utils.Rd:106: missing file link 'Reduce'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-utils.Rd:124: missing file link 'sapply'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-utils.Rd:153: missing file link 'Reduce'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-utils.Rd:180: missing file link 'Reduce'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-utils.Rd:183: missing file link 'within'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-utils.Rd:196: missing file link 'Reduce'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/List-utils.Rd:199: missing file link 'within'
    Pairs-class                             html  
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/Pairs-class.Rd:46: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/Pairs-class.Rd:47: missing file link 'findOverlapPairs'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/Pairs-class.Rd:105: missing file link 'findOverlapPairs'
    Rle-class                               html  
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/Rle-class.Rd:207: missing file link 'IRanges'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/Rle-class.Rd:360: missing file link 'aggregate'
    Rle-runstat                             html  
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/Rle-runstat.Rd:91: missing file link 'RleList-class'
    Rle-utils                               html  
    S4Vectors-internals                     html  
    SimpleList-class                        html  
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/SimpleList-class.Rd:88: missing file link 'CompressedList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/SimpleList-class.Rd:92: missing file link 'SimpleIntegerList'
    Vector-class                            html  
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/Vector-class.Rd:238: missing file link 'CompressedList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/Vector-class.Rd:253: missing file link 'IRanges'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/Vector-class.Rd:254: missing file link 'XRaw'
    Vector-comparison                       html  
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/Vector-comparison.Rd:284: missing file link 'Ranges'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/Vector-comparison.Rd:316: missing file link 'Ranges'
    Vector-setops                           html  
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/Vector-setops.Rd:84: missing file link 'union'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/Vector-setops.Rd:85: missing file link 'intersect'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/Vector-setops.Rd:86: missing file link 'setdiff'
    aggregate-methods                       html  
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/aggregate-methods.Rd:38: missing file link 'end'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/aggregate-methods.Rd:38: missing file link 'width'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/aggregate-methods.Rd:42: missing file link 'RangesList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/aggregate-methods.Rd:43: missing file link 'RangesList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/aggregate-methods.Rd:44: missing file link 'SimpleAtomicList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/aggregate-methods.Rd:95: missing file link 'end'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/aggregate-methods.Rd:96: missing file link 'width'
    expand-methods                          html  
    isSorted                                html  
    shiftApply-methods                      html  
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/shiftApply-methods.Rd:44: missing file link 'window'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/shiftApply-methods.Rd:45: missing file link 'aggregate'
    split-methods                           html  
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/split-methods.Rd:47: missing file link 'splitAsList'
Rd warning: /tmp/RtmpkIj94d/R.INSTALL5a4770ef5339/S4Vectors/man/split-methods.Rd:64: missing file link 'splitAsList'
    str-utils                               html  
    subsetting-utils                        html  
    zip-methods                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (S4Vectors)
Making 'packages.html' ... done