Last data update: 2014.03.03
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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
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