[Seqinr-commits] r1783 - www/src/appendix
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jun 6 12:56:27 CEST 2014
Author: jeanlobry
Date: 2014-06-06 12:56:27 +0200 (Fri, 06 Jun 2014)
New Revision: 1783
Modified:
www/src/appendix/releasenotes.rnw
www/src/appendix/releasenotes.tex
Log:
add an as.string argument so that write.fasta can handle sequences when provided as strings
Modified: www/src/appendix/releasenotes.rnw
===================================================================
--- www/src/appendix/releasenotes.rnw 2014-06-06 10:38:23 UTC (rev 1782)
+++ www/src/appendix/releasenotes.rnw 2014-06-06 10:56:27 UTC (rev 1783)
@@ -5,6 +5,7 @@
\author{Lobry, J.R. \and Nec\c{s}ulea, A. \and Palmeira, L. \and Penel, S.}
\begin{document}
+\SweaveOpts{concordance=TRUE}
\SweaveInput{../config/commonrnw.rnw}
\maketitle
% BEGIN - DO NOT REMOVE THIS LINE
@@ -16,7 +17,7 @@
\section*{3.0 series}
-\subsection{release 3.0-11}
+\subsection*{release 3.0-11}
\begin{itemize}
@@ -26,10 +27,10 @@
\end{itemize}
-\subsection{release 3.0-10}
+\subsection*{release 3.0-10}
-\subsection{release 3.0-0}
+\subsection*{release 3.0-0}
\begin{itemize}
Modified: www/src/appendix/releasenotes.tex
===================================================================
--- www/src/appendix/releasenotes.tex 2014-06-06 10:38:23 UTC (rev 1782)
+++ www/src/appendix/releasenotes.tex 2014-06-06 10:56:27 UTC (rev 1783)
@@ -6,6 +6,7 @@
\usepackage{Sweave}
\begin{document}
+\input{releasenotes-concordance}
%
% To change the R input/output style:
%
@@ -50,8 +51,87 @@
The release notes are listed in reverse chronological order:
most recent on top.
+\section*{3.0 series}
+
+\subsection*{release 3.0-11}
+
+\begin{itemize}
+
+\item Function \texttt{write.fasta()} has gained an \texttt{as.string} argument
+so that it can handle sequences provided as strings instead of vectors of single
+character.
+
+\end{itemize}
+
+\subsection*{release 3.0-10}
+
+
+\subsection*{release 3.0-0}
+
+\begin{itemize}
+
+\item As pointed out by Leonor Palmeira on the \texttt{rpourlesnuls}
+diffusion list on 20-MAY-2010 there was no constructor for objects
+of class alignment. There is now a \texttt{as.alignment()} function.
+\end{itemize}
+
+
\section*{2.0 series}
+\subsection*{release 2.0-9}
+
+\begin{itemize}
+
+\item As pointed out by Avril Coghlan on the seqinR diffusion list on
+17-MAR-2010 there was a bug in the \texttt{getAnnot()} function.
+This is now fixed.
+
+\item As suggested by Avril Coghlan on the seqinR diffusion list on
+02-MAR-2010 the function \texttt{rho()} has gained a \texttt{wordsize}
+argument.
+
+\item The argument \texttt{word} in function \texttt{count()} is
+now more explicitely called \texttt{wordsize}.
+
+\item The example section in file \texttt{read.alignment.Rd} has gained
+a new quality control sanity check.
+
+\item The \texttt{File} argument that was deprecated since seqinR
+release 1.1-3 in function \texttt{read.alignment()} is no more valid.
+Just use \texttt{file} instead.
+
+\item As pointed by Darren Obbard on the seqinr diffusion list on
+05-MAR-2010 there was a memory leak problem when calling the
+\texttt{read.alignment()} function with the fasta format. This
+is now fixed for the fasta format, but the remaining formats have
+not been checked for this problem.
+
+\end{itemize}
+
+\subsection*{release 2.0-8}
+
+\begin{itemize}
+
+\item As pointed by Oliver Clay and Lionel Guy on the seqinr diffusion
+list on 19-FEB-2010 there was a bug in \texttt{getSequence.list()}
+function that confused \texttt{write.fasta()} when all sequences were
+of the same length (a similar bug was reported by Yann Lesecque
+on 30-MAR-2009 for the \texttt{getTrans()} function). This is now
+fixed.
+
+\item The message printed when function \texttt{where.is.this.acc()} fails
+to find a database with a given accession number for a sequence is now
+completed to warn the user that (s)he may have supplied a sequence name
+instead of a genuine accession number.
+
+\item The title in the documentation for the function \texttt{write.fasta()}
+was changed to make clear that more than one sequence can be written at once.
+The function now does not return anything instead of \texttt{NULL} previously.
+The argument \texttt{file.out} was moved to the left so that it is easier now
+to use it by position during function call.
+
+\end{itemize}
+
\subsection*{release 2.0-7}
\begin{itemize}
@@ -390,7 +470,7 @@
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
\end{Soutput}
\begin{Sinput}
- stopifnot(all(resIIIpI == 1))
+ stopifnot(all( resIIIpI == 1))
\end{Sinput}
\end{Schunk}
@@ -647,8 +727,8 @@
letters, some sequences were modified. This should no more be the case:
\begin{Schunk}
\begin{Sinput}
- ali <- list(nb = 4, nam = c("speciesA", "speciesB", "speciesC",
- "speciesD"), seq = c("ACGT", "acgt", "ACGT", "ACGT"))
+ ali <- list(nb=4, nam=c("speciesA", "speciesB", "speciesC", "speciesD"),
+ seq=c("ACGT","acgt","ACGT","ACGT"))
class(ali) <- "alignment"
print(ali$seq)
\end{Sinput}
@@ -925,14 +1005,14 @@
Charif, D. and Lobry, J.R. (2007)
-A BibTeX entry for LaTeX users is
+Une entrée BibTeX pour les utilisateurs LaTeX est
- @incollection{,
+ @InCollection{,
author = {D. Charif and J.R. Lobry},
title = {Seqin{R} 1.0-2: a contributed package to the {R} project for statistical computing devoted to biological sequences retrieval and analysis.},
booktitle = {Structural approaches to sequence evolution: Molecules, networks, populations},
year = {2007},
- editor = {U. Bastolla, M. Porto, H.E. Roman and M. Vendruscolo},
+ editor = {U. Bastolla and M. Porto and H.E. Roman and M. Vendruscolo},
series = {Biological and Medical Physics, Biomedical Engineering},
pages = {207-232},
address = {New York},
@@ -978,20 +1058,20 @@
This part was compiled under the following \Rlogo{}~environment:
\begin{itemize}\raggedright
- \item R version 2.10.0 (2009-10-26), \verb|i386-apple-darwin8.11.1|
- \item Locale: \verb|fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/C/C|
+ \item R version 3.1.0 (2014-04-10), \verb|x86_64-apple-darwin13.1.0|
+ \item Locale: \verb|fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8|
\item Base packages: base, datasets, graphics, grDevices, grid,
methods, stats, utils
- \item Other packages: ade4~1.4-13, ape~2.4, grImport~0.4-4,
- MASS~7.3-3, quadprog~1.4-11, seqinr~2.0-7, tseries~0.10-21,
- XML~2.6-0, xtable~1.5-5, zoo~1.5-8
- \item Loaded via a namespace (and not attached): gee~4.13-14,
- lattice~0.17-26, nlme~3.1-96
+ \item Other packages: ade4~1.6-2, ape~3.1-2, grImport~0.9-0,
+ MASS~7.3-31, seqinr~3.0-10, tseries~0.10-32, XML~3.98-1.1,
+ xtable~1.7-3
+ \item Loaded via a namespace (and not attached): lattice~0.20-29,
+ nlme~3.1-117, quadprog~1.5-5, tools~3.1.0, zoo~1.7-11
\end{itemize}
There were two compilation steps:
\begin{itemize}
- \item \Rlogo{} compilation time was: Sun Nov 15 11:55:18 2009
+ \item \Rlogo{} compilation time was: Fri Jun 6 12:53:58 2014
\item \LaTeX{} compilation time was: \today
\end{itemize}
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