XVector

Package: XVector
Title: Representation and manpulation of external sequences
Description: Memory efficient S4 classes for storing sequences "externally"
(behind an R external pointer, or on disk).
Version: 0.12.0
Encoding: UTF-8
Author: Hervé Pagès and Patrick Aboyoun
Maintainer: Hervé Pagès <hpages@fredhutch.org>
biocViews: Infrastructure, DataRepresentation
Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.11.3), S4Vectors (>=
0.9.29), IRanges (>= 2.5.27)
Imports: methods, zlibbioc, BiocGenerics, S4Vectors, IRanges
LinkingTo: S4Vectors, IRanges
Suggests: Biostrings, drosophila2probe, RUnit
License: Artistic-2.0
Collate: io-utils.R SharedVector-class.R SharedRaw-class.R
SharedInteger-class.R SharedDouble-class.R XVector-class.R
XRaw-class.R XInteger-class.R XDouble-class.R
XVectorList-class.R XRawList-class.R XRawList-comparison.R
XIntegerViews-class.R XDoubleViews-class.R OnDiskRaw-class.R
RdaCollection-class.R intra-range-methods.R compact-methods.R
reverse-methods.R slice-methods.R view-summarization-methods.R
updateObject-methods.R zzz.R
NeedsCompilation: yes
Packaged: 2016-05-04 04:57:18 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'XVector' ...
** 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"   -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"   -fpic  -g -O2  -c Ocopy_byteblocks.c -o Ocopy_byteblocks.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"   -fpic  -g -O2  -c R_init_XVector.c -o R_init_XVector.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"   -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"   -fpic  -g -O2  -c SharedDouble_class.c -o SharedDouble_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"   -fpic  -g -O2  -c SharedInteger_class.c -o SharedInteger_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"   -fpic  -g -O2  -c SharedRaw_class.c -o SharedRaw_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"   -fpic  -g -O2  -c SharedVector_class.c -o SharedVector_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"   -fpic  -g -O2  -c XRawList_comparison.c -o XRawList_comparison.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"   -fpic  -g -O2  -c XVectorList_class.c -o XVectorList_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"   -fpic  -g -O2  -c XVector_class.c -o XVector_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"   -fpic  -g -O2  -c io_utils.c -o io_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"   -fpic  -g -O2  -c slice_methods.c -o slice_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"   -fpic  -g -O2  -c vector_copy.c -o vector_copy.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"   -fpic  -g -O2  -c view_summarization_methods.c -o view_summarization_methods.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o XVector.so IRanges_stubs.o Ocopy_byteblocks.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XRawList_comparison.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -lz -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/XVector/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'toString' from package 'base' in package 'XVector'
** help
*** installing help indices
  converting help for package 'XVector'
    finding HTML links ... done
    OnDiskRaw-class                         html  
    XDoubleViews-class                      html  
Rd warning: /tmp/RtmpYewNdG/R.INSTALL5c241193efa5/XVector/man/XDoubleViews-class.Rd:37: missing file link 'Views'
Rd warning: /tmp/RtmpYewNdG/R.INSTALL5c241193efa5/XVector/man/XDoubleViews-class.Rd:38: missing file link 'Views'
Rd warning: /tmp/RtmpYewNdG/R.INSTALL5c241193efa5/XVector/man/XDoubleViews-class.Rd:39: missing file link 'Views'
    XIntegerViews-class                     html  
Rd warning: /tmp/RtmpYewNdG/R.INSTALL5c241193efa5/XVector/man/XIntegerViews-class.Rd:37: missing file link 'Views'
Rd warning: /tmp/RtmpYewNdG/R.INSTALL5c241193efa5/XVector/man/XIntegerViews-class.Rd:38: missing file link 'Views'
Rd warning: /tmp/RtmpYewNdG/R.INSTALL5c241193efa5/XVector/man/XIntegerViews-class.Rd:39: missing file link 'Views'
    XRawList-class                          html  
    XRawList-comparison                     html  
    XVector-class                           html  
Rd warning: /tmp/RtmpYewNdG/R.INSTALL5c241193efa5/XVector/man/XVector-class.Rd:59: missing file link 'Vector'
Rd warning: /tmp/RtmpYewNdG/R.INSTALL5c241193efa5/XVector/man/XVector-class.Rd:76: missing file link 'XString'
Rd warning: /tmp/RtmpYewNdG/R.INSTALL5c241193efa5/XVector/man/XVector-class.Rd:135: missing file link 'solveUserSEW'
    XVector-internals                       html  
    XVectorList-class                       html  
    compact-methods                         html  
    intra-range-methods                     html  
Rd warning: /tmp/RtmpYewNdG/R.INSTALL5c241193efa5/XVector/man/intra-range-methods.Rd:18: missing file link 'narrow'
Rd warning: /tmp/RtmpYewNdG/R.INSTALL5c241193efa5/XVector/man/intra-range-methods.Rd:18: missing file link 'threebands'
Rd warning: /tmp/RtmpYewNdG/R.INSTALL5c241193efa5/XVector/man/intra-range-methods.Rd:37: missing file link 'solveUserSEW'
Rd warning: /tmp/RtmpYewNdG/R.INSTALL5c241193efa5/XVector/man/intra-range-methods.Rd:64: missing file link 'solveUserSEW'
    reverse-methods                         html  
Rd warning: /tmp/RtmpYewNdG/R.INSTALL5c241193efa5/XVector/man/reverse-methods.Rd:48: missing file link 'endoapply'
    slice-methods                           html  
Rd warning: /tmp/RtmpYewNdG/R.INSTALL5c241193efa5/XVector/man/slice-methods.Rd:14: missing file link 'slice'
Rd warning: /tmp/RtmpYewNdG/R.INSTALL5c241193efa5/XVector/man/slice-methods.Rd:53: missing file link 'IRanges'
    updateObject-methods                    html  
    view-summarization-methods              html  
** building package indices
** testing if installed package can be loaded
* DONE (XVector)
Making 'packages.html' ... done