triplex

Package: triplex
Type: Package
Title: Search and visualize intramolecular triplex-forming sequences in
DNA
Version: 1.12.0
Date: 2013-09-28
Authors@R: c(person("Jiri", "Hon", role = c("aut", "cre"),
email = "jiri.hon@gmail.com"),
person("Matej", "Lexa", role = "aut",
email = "lexa@fi.muni.cz"),
person("Tomas", "Martinek", role = "aut",
email = "martinto@fit.vutbr.cz"),
person("Kamil", "Rajdl", role = "aut"),
person("Daniel", "Kopecek", role = "ctb"))
Author: Jiri Hon, Matej Lexa, Tomas Martinek and Kamil Rajdl with contributions from Daniel Kopecek
Maintainer: Jiri Hon <jiri.hon@gmail.com>
Description: This package provides functions for identification and
visualization of potential intramolecular triplex patterns in DNA sequence.
The main functionality is to detect the positions of subsequences capable of
folding into an intramolecular triplex (H-DNA) in a much larger sequence.
The potential H-DNA (triplexes) should be made of as many cannonical
nucleotide triplets as possible. The package includes visualization showing
the exact base-pairing in 1D, 2D or 3D.
License: BSD_2_clause + file LICENSE
URL: http://www.fi.muni.cz/~lexa/triplex/
biocViews: SequenceMatching, GeneRegulation
Depends: R (>= 2.15.0), S4Vectors (>= 0.5.14), IRanges (>= 2.5.27),
XVector (>= 0.11.6), Biostrings (>= 2.39.10)
Imports: methods, grid, GenomicRanges
Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer,
GenomeGraphs
LinkingTo: S4Vectors, IRanges, XVector, Biostrings
NeedsCompilation: yes
Packaged: 2016-05-05 03:50:37 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'triplex' ...
** 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" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"   -fpic  -g -O2  -c Biostrings_stubs.c -o Biostrings_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" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/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" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"   -fpic  -g -O2  -c R_init_triplex.c -o R_init_triplex.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" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"   -fpic  -g -O2  -c XVector_stubs.c -o XVector_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" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"   -fpic  -g -O2  -c align.c -o align.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" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"   -fpic  -g -O2  -c align_interface.c -o align_interface.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" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"   -fpic  -g -O2  -c dl_list.c -o dl_list.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" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"   -fpic  -g -O2  -c interval.c -o interval.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" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"   -fpic  -g -O2  -c libtriplex.c -o libtriplex.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" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"   -fpic  -g -O2  -c progress.c -o progress.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" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"   -fpic  -g -O2  -c search.c -o search.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" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"   -fpic  -g -O2  -c search_interface.c -o search_interface.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o triplex.so Biostrings_stubs.o IRanges_stubs.o R_init_triplex.o XVector_stubs.o align.o align_interface.o dl_list.o interval.o libtriplex.o progress.o search.o search_interface.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/triplex/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'triplex'
    finding HTML links ... done
    TriplexViews-class                      html  
    finding level-2 HTML links ... done

    ins                                     html  
    lend                                    html  
    lstart                                  html  
    lwidth                                  html  
    pvalue                                  html  
    triplex-package                         html  
    triplex.3D                              html  
    triplex.alignment                       html  
    triplex.diagram                         html  
    triplex.group.table                     html  
    triplex.score.table                     html  
    triplex.search                          html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (triplex)
Making 'packages.html' ... done