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Last data update: 2014.03.03

GenomicTuples

Package: GenomicTuples
Type: Package
Title: Representation and Manipulation of Genomic Tuples
Version: 1.6.2
Date: 2016-04-14
Authors@R: c(person("Peter", "Hickey", role = c("aut", "cre"),
email = "peter.hickey@gmail.com"),
person("Marcin", "Cieslik", role = "ctb",
email = "marcin.cieslik@gmail.com"),
person("Herve", "Pages", role = "ctb"))
Author: Peter Hickey <peter.hickey@gmail.com>, with contributions from Marcin
Cieslik and Herve Pages.
Maintainer: Peter Hickey <peter.hickey@gmail.com>
Description: GenomicTuples defines general purpose containers for storing
genomic tuples. It aims to provide functionality for tuples of genomic
co-ordinates that are analogous to those available for genomic ranges in
the GenomicRanges Bioconductor package.
URL: www.github.com/PeteHaitch/GenomicTuples
BugReports: https://github.com/PeteHaitch/GenomicTuples/issues
biocViews: Infrastructure, DataRepresentation, Sequencing
VignetteBuilder: knitr
Depends: R (>= 3.3.0), GenomicRanges (>= 1.23.15), GenomeInfoDb (>=
1.7.2), S4Vectors (>= 0.9.38)
Imports: methods, BiocGenerics (>= 0.17.0), Rcpp (>= 0.11.2), IRanges
(>= 2.5.26), data.table
Suggests: testthat, knitr, BiocStyle, rmarkdown
LinkingTo: Rcpp
License: Artistic-2.0
Collate: 'AllGenerics.R' 'AllUtilities.R' 'GTuples-class.R'
'GTuples-comparison.R' 'GTuplesList-class.R' 'GenomicTuples.R'
'RcppExports.R' 'coverage-methods.R' 'findOverlaps-methods.R'
'inter-tuple-methods.R' 'intra-tuple-methods.R'
'nearest-methods.R' 'setops-methods.R' 'tile-methods.R' 'zzz.R'
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-16 04:57:31 UTC; biocbuild

● BiocViews: DataRepresentation, Infrastructure, Sequencing
● 0 images, 9 functions, 0 datasets
● Reverse Depends: 0

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'GenomicTuples' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c GenomicTuples_init.c -o GenomicTuples_init.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c IPD.cpp -o IPD.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c allTuplesSorted.cpp -o allTuplesSorted.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c pcompareGTuples.cpp -o pcompareGTuples.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o GenomicTuples.so GenomicTuples_init.o IPD.o RcppExports.o allTuplesSorted.o pcompareGTuples.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/GenomicTuples/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomicTuples'
    finding HTML links ... done
    GTuples-class                           html  
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:75: missing file link 'GRanges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:82: missing file link 'Rle'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:86: missing file link 'IRanges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:91: missing file link 'Rle'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:94: missing file link 'DataFrame'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:101: missing file link 'DataFrame'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:109: missing file link 'GRanges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:132: missing file link 'Rle'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:139: missing file link 'Rle'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:151: missing file link 'DataFrame'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:214: missing file link 'GRanges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:238: missing file link 'Rle'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:267: missing file link 'Rle'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:275: missing file link 'DataFrame'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:278: missing file link 'DataTable'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:291: missing file link 'DataFrame'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:300: missing file link 'seqlevels'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:401: missing file link 'DataFrame'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:402: missing file link 'DataFrame'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:430: missing file link 'Rle'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:509: missing file link 'GRanges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:512: missing file link 'IRanges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:513: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:515: missing file link 'GRanges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:533: missing file link 'GRanges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:534: missing file link 'GAlignments'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:535: missing file link 'GAlignmentPairs'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:538: missing file link 'IRanges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:538: missing file link 'DNAStringSet'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-class.Rd:552: missing file link 'DataFrame'
    GTuples-comparison                      html  
    finding level-2 HTML links ... done

Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuples-comparison.Rd:165: missing file link 'Hits'
    GTuplesList-class                       html  
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuplesList-class.Rd:62: missing file link 'GRangesList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuplesList-class.Rd:100: missing file link 'RleList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuplesList-class.Rd:101: missing file link 'RleList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuplesList-class.Rd:101: missing file link 'CharacterList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuplesList-class.Rd:107: missing file link 'SimpleList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuplesList-class.Rd:113: missing file link 'CompressedIRangesList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuplesList-class.Rd:114: missing file link 'RangesList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuplesList-class.Rd:124: missing file link 'RleList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuplesList-class.Rd:125: missing file link 'RleList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuplesList-class.Rd:126: missing file link 'CharacterList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuplesList-class.Rd:129: missing file link 'RleList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuplesList-class.Rd:130: missing file link 'CharacterList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuplesList-class.Rd:136: missing file link 'DataFrame'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuplesList-class.Rd:156: missing file link 'seqlevels'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuplesList-class.Rd:216: missing file link 'SimpleList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuplesList-class.Rd:252: missing file link 'GRangesList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/GTuplesList-class.Rd:409: missing file link 'RleList-class'
    GenomicTuples-package                   html  
    findOverlaps-methods                    html  
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:102: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:103: missing file link 'Ranges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:103: missing file link 'RangesList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:105: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:106: missing file link 'GRangesList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:108: missing file link 'GAlignments'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:109: missing file link 'GAlignmentPairs'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:110: missing file link 'GAlignmentsList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:140: missing file link 'GRanges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:141: missing file link 'GRangesList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:141: missing file link 'RangesList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:142: missing file link 'RangedData'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:149: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:155: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:198: missing file link 'GRanges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:199: missing file link 'GRangesList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:205: missing file link 'findOverlaps,GRangesList,GRangesList-method'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:218: missing file link 'GRanges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:219: missing file link 'GRangesList'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:233: missing file link 'Hits'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:264: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/findOverlaps-methods.Rd:265: missing file link 'findOverlaps'
    illdefined-methods                      html  
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/illdefined-methods.Rd:56: missing file link 'GRanges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/illdefined-methods.Rd:57: missing file link 'GRangesList'
    intra-tuple-methods                     html  
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/intra-tuple-methods.Rd:43: missing file link 'GRanges'
    nearest-methods                         html  
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/nearest-methods.Rd:26: missing file link 'GRanges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/nearest-methods.Rd:70: missing file link 'Hits'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/nearest-methods.Rd:72: missing file link 'Hits'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/nearest-methods.Rd:147: missing file link 'Hits'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/nearest-methods.Rd:150: missing file link 'Hits'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/nearest-methods.Rd:165: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/nearest-methods.Rd:166: missing file link 'GRanges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/nearest-methods.Rd:167: missing file link 'Ranges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/nearest-methods.Rd:168: missing file link 'Hits'
    tuples-squeezers                        html  
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/tuples-squeezers.Rd:13: missing file link 'granges'
Rd warning: /tmp/RtmpTyCI4u/R.INSTALL5a4a7e1c96df/GenomicTuples/man/tuples-squeezers.Rd:14: missing file link 'grglist'
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomicTuples)
Making 'packages.html' ... done