[Seqinr-commits] r1687 - pkg/inst/doc/src/mainmatter

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

Author: lobry
Date: 2009-11-05 13:43:28 +0100 (Thu, 05 Nov 2009)
New Revision: 1687

Modified:
   pkg/inst/doc/src/mainmatter/extractseqs.tex
Log:
compil R 2.10

Modified: pkg/inst/doc/src/mainmatter/extractseqs.tex
===================================================================
--- pkg/inst/doc/src/mainmatter/extractseqs.tex	2009-11-05 12:24:04 UTC (rev 1686)
+++ pkg/inst/doc/src/mainmatter/extractseqs.tex	2009-11-05 12:43:28 UTC (rev 1687)
@@ -66,11 +66,11 @@
 \end{Sinput}
 \begin{Soutput}
    user  system elapsed 
-  0.083   0.005   5.603 
+  0.123   0.004   5.286 
 \end{Soutput}
 \end{Schunk}
 
-It was then about 6 
+It was then about 5 
 seconds to select the relevant database.
 
 \section{Extacting 78,573 complete human nuclear CDS}
@@ -86,7 +86,7 @@
 \end{Sinput}
 \begin{Soutput}
    user  system elapsed 
-  0.002   0.000  15.358 
+  0.002   0.000  12.499 
 \end{Soutput}
 \begin{Sinput}
  (nseq <- hsCDS$nelem)
@@ -99,15 +99,15 @@
 \end{Sinput}
 \begin{Soutput}
    user  system elapsed 
- 13.876   1.207  96.945 
+ 14.341   1.223 103.048 
 \end{Soutput}
 \end{Schunk}
  
 We have used a virtual query to speed up things:
-it was about 15 seconds 
+it was about 12 seconds 
 to create on the server a list of 78573
 sequences. We have downloaded the sequences in zlib compressed mode:
-it was about 97 seconds
+it was about 103 seconds
 to dowload the sequences in the object \texttt{mycds}, which looks like :
 
 \begin{Schunk}
@@ -143,11 +143,11 @@
 \end{Sinput}
 \begin{Soutput}
    user  system elapsed 
-  0.875   0.732   3.183 
+  3.629   0.783   4.523 
 \end{Soutput}
 \end{Schunk}
 
-It was then about 3 seconds
+It was then about 5 seconds
 to dump the sequences on a local file. We read the sequences as strings
 without setting attributes to save time:
 
@@ -158,11 +158,11 @@
 \end{Sinput}
 \begin{Soutput}
    user  system elapsed 
- 24.219   0.612  25.184 
+ 31.862   0.760  34.040 
 \end{Soutput}
 \end{Schunk}
 
-It was then about 25 seconds
+It was then about 34 seconds
 to read the sequences as strings. We save them in XDR format:
 
 \begin{Schunk}
@@ -171,7 +171,7 @@
 \end{Sinput}
 \begin{Soutput}
    user  system elapsed 
- 41.262   0.319  42.904 
+ 41.165   0.334  42.840 
 \end{Soutput}
 \end{Schunk}
 
@@ -185,7 +185,7 @@
 \end{Sinput}
 \begin{Soutput}
    user  system elapsed 
-  1.378   0.038   1.425 
+  1.374   0.039   1.425 
 \end{Soutput}
 \end{Schunk}
 
@@ -203,11 +203,11 @@
 \end{Sinput}
 \begin{Soutput}
    user  system elapsed 
-  2.642   0.613  52.865 
+  2.906   0.602  55.071 
 \end{Soutput}
 \end{Schunk}
 
-It was then about 53 seconds
+It was then about 55 seconds
 to get the protein sequences from the server. The object \texttt{myprot} looks
 like:
 
@@ -244,11 +244,11 @@
 \end{Sinput}
 \begin{Soutput}
    user  system elapsed 
-  0.331   0.253   0.862 
+  1.324   0.272   1.607 
 \end{Soutput}
 \end{Schunk}
 
-It was then about 1 seconds
+It was then about 2 seconds
 to dump the protein sequences on a local file. We read the sequences as strings
 without setting attributes to save time:
 
@@ -259,11 +259,11 @@
 \end{Sinput}
 \begin{Soutput}
    user  system elapsed 
- 10.283   0.172  10.566 
+ 13.474   0.180  13.744 
 \end{Soutput}
 \end{Schunk}
 
-It was then about 11 seconds
+It was then about 14 seconds
 to read the protein sequences as strings. We save them in XDR format:
 
 \begin{Schunk}
@@ -272,7 +272,7 @@
 \end{Sinput}
 \begin{Soutput}
    user  system elapsed 
-  4.048   0.142   4.214 
+  4.184   0.152   4.358 
 \end{Soutput}
 \end{Schunk}
 
@@ -286,7 +286,7 @@
 \end{Sinput}
 \begin{Soutput}
    user  system elapsed 
-  0.913   0.024   0.942 
+  0.918   0.025   0.948 
 \end{Soutput}
 \end{Schunk}
 
@@ -326,21 +326,21 @@
 
 This part was compiled under the following \Rlogo{}~environment:
 
-\begin{itemize}
-  \item R version 2.9.0 (2009-04-17), \verb|i386-apple-darwin8.11.1|
-  \item Locale: \verb|C|
-  \item Base packages: base, datasets, grDevices, graphics, grid,
+\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 Base packages: base, datasets, graphics, grDevices, grid,
     methods, stats, utils
-  \item Other packages: MASS~7.2-46, XML~2.3-0, ade4~1.4-11,
-    ape~2.3, grImport~0.4-3, quadprog~1.4-11, seqinr~2.0-3,
-    tseries~0.10-18, 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
+  \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
 \end{itemize}
 There were two compilation steps:
 
 \begin{itemize}
-  \item \Rlogo{} compilation time was: Thu Apr 23 11:49:34 2009
+  \item \Rlogo{} compilation time was: Thu Nov  5 13:31:32 2009
   \item \LaTeX{} compilation time was: \today
 \end{itemize}