[Seqinr-commits] r1581 - pkg/inst/doc/src/mainmatter
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Apr 23 11:29:41 CEST 2009
Author: lobry
Date: 2009-04-23 11:29:41 +0200 (Thu, 23 Apr 2009)
New Revision: 1581
Modified:
pkg/inst/doc/src/mainmatter/getseqacnuc.tex
Log:
R 2.9.0 compilation
Modified: pkg/inst/doc/src/mainmatter/getseqacnuc.tex
===================================================================
--- pkg/inst/doc/src/mainmatter/getseqacnuc.tex 2009-04-23 09:27:39 UTC (rev 1580)
+++ pkg/inst/doc/src/mainmatter/getseqacnuc.tex 2009-04-23 09:29:41 UTC (rev 1581)
@@ -5,7 +5,7 @@
\author{Charif, D. \and Lobry, J.R.}
-\usepackage{/Library/Frameworks/R.framework/Resources/share/texmf/Sweave}
+\usepackage{Sweave}
\begin{document}
%
% To change the R input/output style:
@@ -75,12 +75,14 @@
choosebank()
\end{Sinput}
\begin{Soutput}
- [1] "genbank" "embl" "emblwgs" "swissprot" "ensembl"
- [6] "refseq" "nrsub" "hobacnucl" "hobacprot" "hovergendna"
-[11] "hovergen" "hogenom" "hogenomdna" "hogennucl" "hogenprot"
-[16] "hoverclnu" "hoverclpr" "homolens" "homolensdna" "greview"
-[21] "polymorphix" "emglib" "HAMAPnucl" "HAMAPprot" "hoppsigen"
-[26] "nurebnucl" "nurebprot" "taxobacgen"
+ [1] "genbank" "embl" "emblwgs" "swissprot"
+ [5] "ensembl" "refseq" "nrsub" "hobacnucl"
+ [9] "hobacprot" "hovergendna" "hovergen" "hogenom"
+[13] "hogenomdna" "hogennucl" "hogenprot" "hoverclnu"
+[17] "hoverclpr" "homolens3" "homolens3dna" "homolens"
+[21] "homolensdna" "greview" "polymorphix" "emglib"
+[25] "HAMAPnucl" "HAMAPprot" "taxobacgen" "apis"
+[29] "human"
\end{Soutput}
\end{Schunk}
@@ -101,10 +103,10 @@
1 genbank on
2 embl on
3 emblwgs on
- info
-1 GenBank Rel. 167 (15 August 2008) Last Updated: Oct 26, 2008
-2 EMBL Library Release 96 (September 2008) Last Updated: Oct 25, 2008
-3 EMBL Whole Genome Shotgun sequences Release 96 (September 2008)
+ info
+1 GenBank Rel. 171 (15 April 2009) Last Updated: Apr 23, 2009
+2 EMBL Library Release 99 (March 2009) Last Updated: Apr 23, 2009
+3 EMBL Whole Genome Shotgun sequences Release 99 (March 2009)
\end{Soutput}
\end{Schunk}
@@ -162,12 +164,12 @@
.. ..- attr(*, "conn_id")=<externalptr>
$ bankname: chr "genbank"
$ banktype: chr "GENBANK"
- $ totseqs : num 1.02e+08
- $ totspecs: num 598454
- $ totkeys : num 9391212
- $ release : chr " GenBank Rel. 167 (15 August 2008) Last Updated: Oct 26, 2008"
+ $ totseqs : num 1.1e+08
+ $ totspecs: num 637489
+ $ totkeys : num 13783816
+ $ release : chr " GenBank Rel. 171 (15 April 2009) Last Updated: Apr 23, 2009"
$ status :Class 'AsIs' chr "on"
- $ details : chr [1:4] " **** ACNUC Data Base Content **** " " GenBank Rel. 167 (15 August 2008) Last Updated: Oct 26, 2008" "97,378,213,581 bases; 96,406,734 sequences; 5,646,527 subseqs; 525,953 refers." "Software by M. Gouy, Lab. Biometrie et Biologie Evolutive, Universite Lyon I "
+ $ details : chr [1:4] " **** ACNUC Data Base Content **** " " GenBank Rel. 171 (15 April 2009) Last Updated: Apr 23, 2009" "103,287,086,629 bases; 103,570,547 sequences; 6,354,023 subseqs; 549,786 refers." "Software by M. Gouy, Lab. Biometrie et Biologie Evolutive, Universite Lyon I "
\end{Soutput}
\begin{Sinput}
closebank()
@@ -177,15 +179,15 @@
The components of \texttt{banknameSocket} means that in the database
called \texttt{genbank} at the compilation time
of this document there were
-\texttt{102,053,262}
+\texttt{109,924,571}
sequences from
-\texttt{598,454}
+\texttt{637,489}
species and a total of
-\texttt{9,391,212}
+\texttt{13,783,816}
keywords. The status of the bank was
\texttt{on},
and the release information was
-\texttt{ GenBank Rel. 167 (15 August 2008) Last Updated: Oct 26, 2008}.
+\texttt{ GenBank Rel. 171 (15 April 2009) Last Updated: Apr 23, 2009}.
For specialized databases, some relevant informations are also given in the
\texttt{details} component, for instance:
@@ -381,15 +383,15 @@
allcds$nelem
\end{Sinput}
\begin{Soutput}
-[1] 6067613
+[1] 6900945
\end{Soutput}
\end{Schunk}
-There are therefore \texttt{6,067,613} coding
+There are therefore \texttt{6,900,945} coding
sequences in this version of GenBank\footnote{
which is stored in the \texttt{release} component of the object \texttt{banknameSocket}
and current value is today (\today): \texttt{banknameSocket\$release =
- GenBank Rel. 167 (15 August 2008) Last Updated: Oct 26, 2008}.
+ GenBank Rel. 171 (15 April 2009) Last Updated: Apr 23, 2009}.
}.
It would be long to get all the informations for the elements
of this list, so we have set the parameter \texttt{virtual} to \texttt{TRUE} and the \texttt{req}
@@ -416,11 +418,11 @@
small$nelem
\end{Sinput}
\begin{Soutput}
-[1] 935
+[1] 956
\end{Soutput}
\end{Schunk}
-There are then \texttt{935} elements in
+There are then \texttt{956} elements in
the list \texttt{small}, so that we can safely repeat the previous query without asking for a
virtual list:
@@ -446,10 +448,10 @@
man$nelem
\end{Sinput}
\begin{Soutput}
-[1] 11551823
+[1] 12404202
\end{Soutput}
\end{Schunk}
-There are \texttt{11,551,823} sequences from \textit{Homo sapiens}.
+There are \texttt{12,404,202} sequences from \textit{Homo sapiens}.
\item[\textbf{Sex.}] How many sequences are annotated with a keyword starting by sex?
\begin{Schunk}
@@ -458,10 +460,10 @@
sex$nelem
\end{Sinput}
\begin{Soutput}
-[1] 1346
+[1] 1397
\end{Soutput}
\end{Schunk}
-There are \texttt{1,346} such sequences.
+There are \texttt{1,397} such sequences.
\item[\textbf{tRNA.}] How many complete tRNA sequences are available?
\begin{Schunk}
@@ -470,10 +472,10 @@
trna$nelem
\end{Sinput}
\begin{Soutput}
-[1] 324327
+[1] 358411
\end{Soutput}
\end{Schunk}
-There are \texttt{324,327} complete tRNA sequences.
+There are \texttt{358,411} complete tRNA sequences.
\item[\textbf{Nature vs. Science.}] In which journal were the more sequences published?
\begin{Schunk}
@@ -482,19 +484,19 @@
nature$nelem
\end{Sinput}
\begin{Soutput}
-[1] 1740183
+[1] 1954774
\end{Soutput}
\begin{Sinput}
query("science", "j=science", virtual = T)
science$nelem
\end{Sinput}
\begin{Soutput}
-[1] 1338780
+[1] 1341474
\end{Soutput}
\end{Schunk}
-There are \texttt{1,740,183} sequences published
+There are \texttt{1,954,774} sequences published
in \textit{Nature} and
-\texttt{1,338,780} sequences published in
+\texttt{1,341,474} sequences published in
\textit{Science}, so that the winner is
\textit{Nature}.
@@ -509,10 +511,10 @@
smith$nelem
\end{Sinput}
\begin{Soutput}
-[1] 4183000
+[1] 4754303
\end{Soutput}
\end{Schunk}
-There are \texttt{4,183,000} such sequences.
+There are \texttt{4,754,303} such sequences.
\item[\textbf{YK2.}] How many sequences were published after year 2000 (included)?
\begin{Schunk}
@@ -521,10 +523,10 @@
yk2$nelem
\end{Sinput}
\begin{Soutput}
-[1] 84819267
+[1] 91981106
\end{Soutput}
\end{Schunk}
-There are \texttt{84,819,267} sequences published after year 2000.
+There are \texttt{91,981,106} sequences published after year 2000.
\item[\textbf{Organelle contest.}] Do we have more sequences from chloroplast genomes or from mitochondion genomes?
\begin{Schunk}
@@ -533,19 +535,19 @@
chloro$nelem
\end{Sinput}
\begin{Soutput}
-[1] 197367
+[1] 223109
\end{Soutput}
\begin{Sinput}
query("mito", "o=mitochondrion", virtual = T)
mito$nelem
\end{Sinput}
\begin{Soutput}
-[1] 650254
+[1] 721261
\end{Soutput}
\end{Schunk}
-There are \texttt{197,367} sequences from
+There are \texttt{223,109} sequences from
chloroplast genomes and
-\texttt{650,254} sequences from mitochondrion
+\texttt{721,261} sequences from mitochondrion
genomes, so that the winner is
mitochondrion.
@@ -845,26 +847,30 @@
\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 17:59:06 2008
+ \item \Rlogo{} compilation time was: Thu Apr 23 11:29:00 2009
\item \LaTeX{} compilation time was: \today
\end{itemize}
+\end{scriptsize}
+
% END - DO NOT REMOVE THIS LINE
%%%%%%%%%%%% BIBLIOGRAPHY %%%%%%%%%%%%%%%%%
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