AlignStat

Package: AlignStat
Type: Package
Title: Comparison of Alternative Multiple Sequence Alignments
Version: 1.2.1
Date: 2016-05-21
Author: Thomas Shafee, Ira Cooke
Maintainer: Thomas Shafee <thomas.shafee@gmail.com>
URL: https://github.com/TS404/AlignStat
BugReports: https://github.com/TS404/AlignStat/issues
Description: Methods for comparing two alternative multiple
sequence alignments (MSAs) to determine whether they align homologous residues in
the same columns as one another. It then classifies similarities and differences
into conserved gaps, conserved sequence, merges, splits or shifts of one MSA relative
to the other. Summarising these categories for each MSA column yields information
on which sequence regions are agreed upon my both MSAs, and which differ. Several
plotting functions enable easily visualisation of the comparison data for analysis.
License: GPL (>= 2)
Depends: R (>= 2.10)
Imports: Rcpp (>= 0.11.6), seqinr, ggplot2, reshape2, tools, utils
LinkingTo: Rcpp
Suggests: testthat
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-24 11:25:31 UTC; icooke
Repository: CRAN
Date/Publication: 2016-05-24 14:49:45

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'AlignStat' ...
** package 'AlignStat' successfully unpacked and MD5 sums checked
** libs
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 rcpp_align.cpp -o rcpp_align.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o AlignStat.so RcppExports.o rcpp_align.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/AlignStat/libs
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'AlignStat'
    finding HTML links ... done
    AlignStat                               html  
    compare_alignments                      html  
    comparison_alignment                    html  
    plot_SP_summary                         html  
    plot_dissimilarity_matrix               html  
    plot_dissimilarity_summary              html  
    plot_similarity_heatmap                 html  
    plot_similarity_summary                 html  
    reference_alignment                     html  
** building package indices
** testing if installed package can be loaded
* DONE (AlignStat)
Making 'packages.html' ... done