[Seqinr-commits] r1579 - pkg/inst/doc/src/mainmatter

[noreply at r-forge.r-project.org]

Author: lobry
Date: 2009-04-23 10:58:39 +0200 (Thu, 23 Apr 2009)
New Revision: 1579

Modified:
   pkg/inst/doc/src/mainmatter/introduction.tex
Log:
compilation R 2.9.0

Modified: pkg/inst/doc/src/mainmatter/introduction.tex
===================================================================
--- pkg/inst/doc/src/mainmatter/introduction.tex	2009-04-23 08:57:43 UTC (rev 1578)
+++ pkg/inst/doc/src/mainmatter/introduction.tex	2009-04-23 08:58:39 UTC (rev 1579)
@@ -4,7 +4,7 @@
 \title{Introduction}
 \author{Lobry, J.R.}
 
-\usepackage{/Library/Frameworks/R.framework/Resources/share/texmf/Sweave}
+\usepackage{Sweave}
 \begin{document}
 %
 % To change the R input/output style:
@@ -134,8 +134,8 @@
 \end{Sinput}
 \begin{Soutput}
 [1] "             ****     ACNUC Data Base Content      ****                         "
-[2] "          GenBank Rel. 167 (15 August 2008) Last Updated: Oct 26, 2008"          
-[3] "97,378,213,581 bases; 96,406,734 sequences; 5,646,527 subseqs; 525,953 refers."  
+[2] "          GenBank Rel. 171 (15 April 2009) Last Updated: Apr 23, 2009"           
+[3] "103,287,086,629 bases; 103,570,547 sequences; 6,354,023 subseqs; 549,786 refers."
 [4] "Software by M. Gouy, Lab. Biometrie et Biologie Evolutive, Universite Lyon I "   
 \end{Soutput}
 \begin{Sinput}
@@ -143,7 +143,7 @@
  bpbk
 \end{Sinput}
 \begin{Soutput}
-[1] "97,378,213,581"
+[1] "103,287,086,629"
 \end{Soutput}
 \begin{Sinput}
  bpbk <- as.numeric(paste(unlist(strsplit(bpbk, split = ",")), 
@@ -152,11 +152,11 @@
  (widthkm <- widthcm/10^5)
 \end{Sinput}
 \begin{Soutput}
-[1] 8.32283
+[1] 8.827856
 \end{Soutput}
 \end{Schunk}
 
-It would be about 8.3
+It would be about 8.8
 kilometer long in ACNUC book format to print GenBank today (\today). As a
 matter of comparison, our local universitary library buiding\footnote{
 Université de Lyon, F-69000, Lyon ; Université Lyon 1 ; 
@@ -183,9 +183,9 @@
 The Comprehensive \Rlogo{} Archive Network, CRAN, is a network of servers 
 around the world that store identical, up-to-date, versions of code and documentation 
 for R. At compilation time of this document, there were
-56 
+61 
 mirrors available 
-from 34 countries.
+from 36 countries.
 Please use the CRAN mirror nearest to you to minimize network load, they are
 listed at \texttt{http://cran.r-project.org/mirrors.html}, and can be directly
 selected with the function \texttt{chooseCRANmirror()}.
@@ -195,8 +195,8 @@
 In the terminology of the \Rlogo{} project \cite{R, RfromR}, this document 
 is a package \emph{vignette}, which means that all code outputs present 
 here were actually obtained by runing them.
-The examples given thereafter were run under \texttt{R version 2.8.0 (2008-10-20)}
-on Sun Oct 26 17:49:56 2008 with Sweave \cite{Sweave}. There is a section at the end of
+The examples given thereafter were run under \texttt{R version 2.9.0 (2009-04-17)}
+on Thu Apr 23 10:54:59 2009 with Sweave \cite{Sweave}. There is a section at the end of
 each chapter called \textbf{Session Informations} that gives details about
 packages and package versions that were involved\footnote{
 Previous versions of \Rlogo{} and packages are available on CRAN mirrors,
@@ -251,8 +251,9 @@
  lseqinr()[1:9]
 \end{Sinput}
 \begin{Soutput}
-[1] "AAstat"      "EXP"         "GC"          "GC1"         "GC2"        
-[6] "GC3"         "GCpos"       "SEQINR.UTIL" "a"          
+[1] "a"            "aaa"          "AAstat"       "acnucclose"  
+[5] "acnucopen"    "al2bp"        "alllistranks" "alr"         
+[9] "amb"         
 \end{Soutput}
 \end{Schunk}
 
@@ -302,7 +303,7 @@
 
 Do not re-invent (there's a patent \cite{wheel} on it anyway).
 At the compilation time of this document there were 
-1559
+1753
 contributed packages available. Even if you don't want to be spoon-feed 
 \textit{{\`a} bouche ouverte}, 
 it's not a bad
@@ -451,7 +452,7 @@
 \setkeys{Gin}{width=0.8\textwidth}
 
 
-The doubling time is now 16.7 months.
+The doubling time is now 16.8 months.
 
 
 \begin{figure}
@@ -478,26 +479,30 @@
 
 \section*{Session Informations}
 
+\begin{scriptsize}
+
 This part was compiled under the following \Rlogo{}~environment:
 
 \begin{itemize}
-  \item R version 2.8.0 (2008-10-20), \verb|i386-apple-darwin8.8.2|
+  \item R version 2.9.0 (2009-04-17), \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 Base packages: base, datasets, grDevices, graphics, methods,
-    stats, utils
-  \item Other packages: MASS~7.2-44, ade4~1.4-9, ape~2.2-2,
-    nlme~3.1-89, quadprog~1.4-11, seqinr~2.0-0, tseries~0.10-16,
-    xtable~1.5-4, zoo~1.5-4
-  \item Loaded via a namespace (and not attached): grid~2.8.0,
-    lattice~0.17-15, tools~2.8.0
+  \item Base packages: base, datasets, graphics, grDevices, grid,
+    methods, stats, utils
+  \item Other packages: ade4~1.4-11, ape~2.3, grImport~0.4-3,
+    MASS~7.2-46, quadprog~1.4-11, seqinr~2.0-3, tseries~0.10-18,
+    XML~2.3-0, xtable~1.5-5, zoo~1.5-5
+  \item Loaded via a namespace (and not attached): gee~4.13-13,
+    lattice~0.17-22, nlme~3.1-90, tools~2.9.0
 \end{itemize}
 There were two compilation steps:
 
 \begin{itemize}
-  \item \Rlogo{} compilation time was: Sun Oct 26 17:50:03 2008
+  \item \Rlogo{} compilation time was: Thu Apr 23 10:55:04 2009
   \item \LaTeX{} compilation time was: \today
 \end{itemize}
 
+\end{scriptsize}
+
 % END - DO NOT REMOVE THIS LINE
 
 %%%%%%%%%%%%  BIBLIOGRAPHY %%%%%%%%%%%%%%%%%