[Seqinr-commits] r1484 - pkg/inst/doc/src/mainmatter
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Oct 26 18:31:30 CET 2008
Author: lobry
Date: 2008-10-26 18:31:30 +0100 (Sun, 26 Oct 2008)
New Revision: 1484
Modified:
pkg/inst/doc/src/mainmatter/acnucsocket.tex
pkg/inst/doc/src/mainmatter/extractseqs.tex
pkg/inst/doc/src/mainmatter/multivariate.tex
pkg/inst/doc/src/mainmatter/nonparastats.tex
pkg/inst/doc/src/mainmatter/querylang.tex
pkg/inst/doc/src/mainmatter/risa.tex
Log:
R 2.8.0
Modified: pkg/inst/doc/src/mainmatter/acnucsocket.tex
===================================================================
--- pkg/inst/doc/src/mainmatter/acnucsocket.tex 2008-10-26 17:30:17 UTC (rev 1483)
+++ pkg/inst/doc/src/mainmatter/acnucsocket.tex 2008-10-26 17:31:30 UTC (rev 1484)
@@ -397,7 +397,7 @@
cat(dbplaces, sep = "\n")
\end{Sinput}
\begin{Soutput}
-setenv demoacnuc '/Users/lobry/seqinr/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/demoacnuc/index /Users/lobry/seqinr/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/demoacnuc/flat_files'
+setenv demoacnuc '/Users/lobry/seqinr/pkg/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/demoacnuc/index /Users/lobry/seqinr/pkg/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/demoacnuc/flat_files'
\end{Soutput}
\end{Schunk}
@@ -415,16 +415,16 @@
system("ps | grep racnucd", intern = TRUE)
\end{Sinput}
\begin{Soutput}
-[1] " 9415 p2 S+ 0:00.01 ./racnucd racnucd.new"
-[2] " 9416 p2 S+ 0:00.01 sh -c ps | grep racnucd"
-[3] " 9418 p2 S+ 0:00.00 grep racnucd"
+[1] "28875 p3 S+ 0:00.01 ./racnucd racnucd.new"
+[2] "28876 p3 S+ 0:00.01 sh -c ps | grep racnucd"
+[3] "28878 p3 S+ 0:00.00 grep racnucd"
\end{Soutput}
\begin{Sinput}
cat(readLines("racnucd.log"), sep = "\n")
\end{Sinput}
\begin{Soutput}
*******************************************************
-Start of remote acnuc server : Mon May 12 18:24:47 2008
+Start of remote acnuc server : Sun Oct 26 18:13:16 2008
\end{Soutput}
\begin{Sinput}
setwd(pwd)
@@ -686,36 +686,36 @@
\begin{Soutput}
Build a protein database in:
============================
- ->/Users/lobry/seqinr/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb
+ ->/Users/lobry/seqinr/pkg/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb
ACNUC environment:
- ->/Users/lobry/seqinr/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/index
- ->/Users/lobry/seqinr/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/flat_files
+ ->/Users/lobry/seqinr/pkg/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/index
+ ->/Users/lobry/seqinr/pkg/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/flat_files
ACNUC tools in:
- ->/Users/lobry/seqinr/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/../../ACNUC_SOFT/tools
+ ->/Users/lobry/seqinr/pkg/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/../../ACNUC_SOFT/tools
flat file: escherichia_uniprot.dat
- ->/Users/lobry/seqinr/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/flat_files/escherichia_uniprot.dat
+ ->/Users/lobry/seqinr/pkg/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/flat_files/escherichia_uniprot.dat
Begin to build index...
-Mon May 12 18:25:29 CEST 2008
+Sun Oct 26 18:13:52 CET 2008
=====================================
Initialise
Normal end.
=====================================
Generation des index
-Program started at Mon May 12 18:25:31 2008
+Program started at Sun Oct 26 18:13:53 2008
New division created: escherichia_uniprot
Removing updated sequences
0 modified sequences removed
-Loading acc nos started at Mon May 12 18:25:31 2008
-finished at Mon May 12 18:25:31 2008
+Loading acc nos started at Sun Oct 26 18:13:53 2008
+finished at Sun Oct 26 18:13:53 2008
Start loading ncbi species taxonomy
Warning: file $acnuctaxo/id.report not found
-Sequence loading started at Mon May 12 18:25:31 2008
+Sequence loading started at Sun Oct 26 18:13:53 2008
---->3MG1_ECOLI
---->3MG2_ECOLI
@@ -739,12 +739,12 @@
cat(tail(readLines("build.log"), 50), sep = "\n")
\end{Sinput}
\begin{Soutput}
-Program finished at Mon May 12 18:25:35 2008
+Program finished at Sun Oct 26 18:13:56 2008
write_quick_meres...done
lues=4461 chargees=4461 difference=0
-seqs/second=1115.25
+seqs/second=1487.00
=====================================
run newordalphab
@@ -770,7 +770,7 @@
=====================================
run updatehelp
-Mon May 12 18:25:39 CEST 2008
+Sun Oct 26 18:13:58 CET 2008
Index have been sucessfully build.
=====================================
@@ -884,7 +884,7 @@
(seqinrloc <- normalizePath(.path.package("seqinr")))
\end{Sinput}
\begin{Soutput}
-[1] "/Users/lobry/seqinr.Rcheck/seqinr"
+[1] "/Users/lobry/seqinr/pkg.Rcheck/seqinr"
\end{Soutput}
\begin{Sinput}
setwd(seqinrloc)
@@ -900,11 +900,8 @@
dir()
\end{Sinput}
\begin{Soutput}
-[1] "atxy.sty" "authors.tex"
-[3] "book.bib" "book.bib.~1.1.2.31.~"
-[5] "commonrnw.rnw" "commonrnw.rnw.~1.1.2.2.~"
-[7] "commontex.tex" "sessionInfo.rnw"
-[9] "sessionInfo.rnw.~1.1.2.2.~"
+[1] "atxy.sty" "book.bib" "commonrnw.rnw" "commontex.tex"
+[5] "sessionInfo.rnw"
\end{Soutput}
\begin{Sinput}
cat(readLines("book.bib", n = 5), sep = "\n")
@@ -928,19 +925,20 @@
This part was compiled under the following \Rlogo{}~environment:
\begin{itemize}
- \item R version 2.8.0 Under development (unstable) (2008-05-11 r45672), \verb|i386-apple-darwin8.8.2|
+ \item R version 2.8.0 (2008-10-20), \verb|i386-apple-darwin8.8.2|
\item Locale: \verb|C|
\item Base packages: base, datasets, grDevices, graphics, methods,
stats, utils
- \item Other packages: MASS~7.2-42, ade4~1.4-7, ape~2.2,
- nlme~3.1-88, seqinr~1.1-6, xtable~1.5-2
+ \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~0.17-7, tools~2.8.0
+ lattice~0.17-15, tools~2.8.0
\end{itemize}
There were two compilation steps:
\begin{itemize}
- \item \Rlogo{} compilation time was: Mon May 12 18:25:39 2008
+ \item \Rlogo{} compilation time was: Sun Oct 26 18:13:58 2008
\item \LaTeX{} compilation time was: \today
\end{itemize}
Modified: pkg/inst/doc/src/mainmatter/extractseqs.tex
===================================================================
--- pkg/inst/doc/src/mainmatter/extractseqs.tex 2008-10-26 17:30:17 UTC (rev 1483)
+++ pkg/inst/doc/src/mainmatter/extractseqs.tex 2008-10-26 17:31:30 UTC (rev 1484)
@@ -66,11 +66,11 @@
\end{Sinput}
\begin{Soutput}
user system elapsed
- 0.078 0.002 5.451
+ 0.073 0.002 5.550
\end{Soutput}
\end{Schunk}
-It was then about 5
+It was then about 6
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 10.054
+ 0.001 0.000 12.840
\end{Soutput}
\begin{Sinput}
(nseq <- hsCDS$nelem)
@@ -99,15 +99,15 @@
\end{Sinput}
\begin{Soutput}
user system elapsed
- 14.638 1.420 90.581
+ 13.884 1.350 88.041
\end{Soutput}
\end{Schunk}
We have used a virtual query to speed up things:
-it was about 10 seconds
+it was about 13 seconds
to create on the server a list of 78573
sequences. We have downloaded the sequences in zlib compressed mode:
-it was about 91 seconds
+it was about 88 seconds
to dowload the sequences in the object \texttt{mycds}, which looks like :
\begin{Schunk}
@@ -143,7 +143,7 @@
\end{Sinput}
\begin{Soutput}
user system elapsed
- 0.887 0.741 2.875
+ 0.883 0.816 3.471
\end{Soutput}
\end{Schunk}
@@ -158,11 +158,11 @@
\end{Sinput}
\begin{Soutput}
user system elapsed
- 25.853 0.703 28.019
+ 23.774 0.644 25.491
\end{Soutput}
\end{Schunk}
-It was then about 28 seconds
+It was then about 25 seconds
to read the sequences as strings. We save them in XDR format:
\begin{Schunk}
@@ -171,11 +171,11 @@
\end{Sinput}
\begin{Soutput}
user system elapsed
- 40.935 0.357 42.696
+ 41.192 0.330 42.113
\end{Soutput}
\end{Schunk}
-It was then about 43 seconds
+It was then about 42 seconds
to save the sequences in XDR format. How long is it to load the sequences
from XDR format?
@@ -185,7 +185,7 @@
\end{Sinput}
\begin{Soutput}
user system elapsed
- 1.378 0.042 1.459
+ 1.367 0.038 1.427
\end{Soutput}
\end{Schunk}
@@ -203,7 +203,7 @@
\end{Sinput}
\begin{Soutput}
user system elapsed
- 2.912 0.700 56.590
+ 2.846 0.651 57.206
\end{Soutput}
\end{Schunk}
@@ -244,7 +244,7 @@
\end{Sinput}
\begin{Soutput}
user system elapsed
- 0.338 0.264 1.055
+ 0.334 0.288 1.017
\end{Soutput}
\end{Schunk}
@@ -259,11 +259,11 @@
\end{Sinput}
\begin{Soutput}
user system elapsed
- 11.247 0.195 11.679
+ 10.366 0.183 10.745
\end{Soutput}
\end{Schunk}
-It was then about 12 seconds
+It was then about 11 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
- 4.068 0.150 4.270
+ 4.087 0.166 4.317
\end{Soutput}
\end{Schunk}
@@ -286,7 +286,7 @@
\end{Sinput}
\begin{Soutput}
user system elapsed
- 0.920 0.027 0.955
+ 0.917 0.029 0.992
\end{Soutput}
\end{Schunk}
@@ -325,19 +325,20 @@
This part was compiled under the following \Rlogo{}~environment:
\begin{itemize}
- \item R version 2.8.0 Under development (unstable) (2008-05-11 r45672), \verb|i386-apple-darwin8.8.2|
+ \item R version 2.8.0 (2008-10-20), \verb|i386-apple-darwin8.8.2|
\item Locale: \verb|C|
\item Base packages: base, datasets, grDevices, graphics, methods,
stats, utils
- \item Other packages: MASS~7.2-42, ade4~1.4-7, ape~2.2,
- nlme~3.1-88, seqinr~1.1-6, xtable~1.5-2
+ \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~0.17-7
+ lattice~0.17-15
\end{itemize}
There were two compilation steps:
\begin{itemize}
- \item \Rlogo{} compilation time was: Mon May 12 18:21:19 2008
+ \item \Rlogo{} compilation time was: Sun Oct 26 18:10:20 2008
\item \LaTeX{} compilation time was: \today
\end{itemize}
Modified: pkg/inst/doc/src/mainmatter/multivariate.tex
===================================================================
--- pkg/inst/doc/src/mainmatter/multivariate.tex 2008-10-26 17:30:17 UTC (rev 1483)
+++ pkg/inst/doc/src/mainmatter/multivariate.tex 2008-10-26 17:31:30 UTC (rev 1484)
@@ -931,19 +931,20 @@
This part was compiled under the following \Rlogo{}~environment:
\begin{itemize}
- \item R version 2.8.0 Under development (unstable) (2008-05-11 r45672), \verb|i386-apple-darwin8.8.2|
+ \item R version 2.8.0 (2008-10-20), \verb|i386-apple-darwin8.8.2|
\item Locale: \verb|C|
\item Base packages: base, datasets, grDevices, graphics, methods,
stats, utils
- \item Other packages: MASS~7.2-42, ade4~1.4-7, ape~2.2,
- nlme~3.1-88, seqinr~1.1-6, xtable~1.5-2
+ \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~0.17-7, tools~2.8.0
+ lattice~0.17-15, tools~2.8.0
\end{itemize}
There were two compilation steps:
\begin{itemize}
- \item \Rlogo{} compilation time was: Mon May 12 18:32:21 2008
+ \item \Rlogo{} compilation time was: Sun Oct 26 18:14:47 2008
\item \LaTeX{} compilation time was: \today
\end{itemize}
Modified: pkg/inst/doc/src/mainmatter/nonparastats.tex
===================================================================
--- pkg/inst/doc/src/mainmatter/nonparastats.tex 2008-10-26 17:30:17 UTC (rev 1483)
+++ pkg/inst/doc/src/mainmatter/nonparastats.tex 2008-10-26 17:31:30 UTC (rev 1484)
@@ -204,7 +204,7 @@
tail(appli)
\end{Sinput}
\begin{Soutput}
-[1] TRUE TRUE FALSE FALSE FALSE TRUE
+[1] TRUE TRUE TRUE FALSE TRUE FALSE
\end{Soutput}
\end{Schunk}
@@ -300,7 +300,7 @@
SR(appli)$stat
\end{Sinput}
\begin{Soutput}
-[1] 10.81602
+[1] 10.08087
\end{Soutput}
\end{Schunk}
@@ -378,7 +378,7 @@
VR(appli)$stat
\end{Sinput}
\begin{Soutput}
-[1] 4.587283
+[1] 4.618334
\end{Soutput}
\end{Schunk}
@@ -468,7 +468,7 @@
CC(appli)$stat
\end{Sinput}
\begin{Soutput}
-[1] 3.266275
+[1] 3.748402
\end{Soutput}
\end{Schunk}
@@ -544,7 +544,7 @@
NS(appli)$stat
\end{Sinput}
\begin{Soutput}
-[1] -33.78859
+[1] -33.75721
\end{Soutput}
\end{Schunk}
@@ -627,7 +627,7 @@
GM(appli)$stat
\end{Sinput}
\begin{Soutput}
-[1] 320.8337
+[1] 301.4908
\end{Soutput}
\end{Schunk}
@@ -1291,20 +1291,20 @@
This part was compiled under the following \Rlogo{}~environment:
\begin{itemize}
- \item R version 2.7.1 (2008-06-23), \verb|i386-apple-darwin8.8.2|
- \item Locale: \verb|fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/C/C|
+ \item R version 2.8.0 (2008-10-20), \verb|i386-apple-darwin8.8.2|
+ \item Locale: \verb|C|
\item Base packages: base, datasets, grDevices, graphics, methods,
stats, utils
- \item Other packages: MASS~7.2-42, ade4~1.4-9, ape~2.2-1,
- nlme~3.1-89, quadprog~1.4-11, seqinr~1.1-7, tseries~0.10-15,
- xtable~1.5-2, zoo~1.5-4
- \item Loaded via a namespace (and not attached): grid~2.7.1,
- lattice~0.17-8, tools~2.7.1
+ \item Other packages: MASS~7.2-44, ade4~1.4-9, ape~2.2-2,
+ nlme~3.1-89, quadprog~1.4-11, seqinr~2.0-0, tseries~0.10-16,
+ xtable~1.5-4, zoo~1.5-4
+ \item Loaded via a namespace (and not attached): grid~2.8.0,
+ lattice~0.17-15, tools~2.8.0
\end{itemize}
There were two compilation steps:
\begin{itemize}
- \item \Rlogo{} compilation time was: Thu Jul 17 14:47:41 2008
+ \item \Rlogo{} compilation time was: Sun Oct 26 18:24:10 2008
\item \LaTeX{} compilation time was: \today
\end{itemize}
Modified: pkg/inst/doc/src/mainmatter/querylang.tex
===================================================================
--- pkg/inst/doc/src/mainmatter/querylang.tex 2008-10-26 17:30:17 UTC (rev 1483)
+++ pkg/inst/doc/src/mainmatter/querylang.tex 2008-10-26 17:31:30 UTC (rev 1484)
@@ -195,7 +195,7 @@
hsn$nelem
\end{Sinput}
\begin{Soutput}
-[1] 1338
+[1] 1339
\end{Soutput}
\begin{Sinput}
query("hsnsp", "PS hsn")
@@ -534,10 +534,10 @@
\end{Sinput}
\begin{Soutput}
sname libel
-3756 CHLOROPLAST Chloroplast genome
-3757 MITOCHONDRION Mitochondrial genome
-3758 NUCLEOMORPH Nucleomorph genome
-3759 PLASTID non-green plastid genome
+3827 CHLOROPLAST Chloroplast genome
+3828 MITOCHONDRION Mitochondrial genome
+3829 NUCLEOMORPH Nucleomorph genome
+3830 PLASTID non-green plastid genome
\end{Soutput}
\begin{Sinput}
closebank()
@@ -623,16 +623,17 @@
"libel")]
\end{Sinput}
\begin{Soutput}
- sname libel
-1 ANN Annotated CON data class
-2 EST Expressed Sequence Tags data class
-3 GSS Genome Survey Sequence data class
-4 HTC High Throughput cDNA data class
-5 HTG High Throughput Genome sequencing data class
-6 PAT Patent data class
-7 STD standard data class
-8 STS Sequence Tagged Site data class
-9 TPA Third Party Annotation data class
+ sname libel
+1 ANN Annotated CON data class
+2 EST Expressed Sequence Tags data class
+3 GSS Genome Survey Sequence data class
+4 HTC High Throughput cDNA data class
+5 HTG High Throughput Genome sequencing data class
+6 PAT Patent data class
+7 STD standard data class
+8 STS Sequence Tagged Site data class
+9 TPA Third Party Annotation data class
+10 TSA Transcriptome Shotgun Assembly data class
\end{Soutput}
\begin{Sinput}
closebank()
@@ -661,7 +662,7 @@
STexample$nelem
\end{Sinput}
\begin{Soutput}
-[1] 362782
+[1] 392667
\end{Soutput}
\begin{Sinput}
closebank()
@@ -1183,19 +1184,20 @@
This part was compiled under the following \Rlogo{}~environment:
\begin{itemize}
- \item R version 2.8.0 Under development (unstable) (2008-05-11 r45672), \verb|i386-apple-darwin8.8.2|
- \item Locale: \verb|C|
+ \item R version 2.8.0 (2008-10-20), \verb|i386-apple-darwin8.8.2|
+ \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~7.2-42, ade4~1.4-7, ape~2.2,
- nlme~3.1-88, seqinr~1.1-6, xtable~1.5-2
+ \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~0.17-7, tools~2.8.0
+ lattice~0.17-15, tools~2.8.0
\end{itemize}
There were two compilation steps:
\begin{itemize}
- \item \Rlogo{} compilation time was: Mon May 12 18:14:12 2008
+ \item \Rlogo{} compilation time was: Sun Oct 26 18:04:21 2008
\item \LaTeX{} compilation time was: \today
\end{itemize}
Modified: pkg/inst/doc/src/mainmatter/risa.tex
===================================================================
--- pkg/inst/doc/src/mainmatter/risa.tex 2008-10-26 17:30:17 UTC (rev 1483)
+++ pkg/inst/doc/src/mainmatter/risa.tex 2008-10-26 17:31:30 UTC (rev 1484)
@@ -617,20 +617,20 @@
This part was compiled under the following \Rlogo{}~environment:
\begin{itemize}
- \item R version 2.7.2 (2008-08-25), \verb|i386-apple-darwin8.8.2|
- \item Locale: \verb|fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/C/C|
+ \item R version 2.8.0 (2008-10-20), \verb|i386-apple-darwin8.8.2|
+ \item Locale: \verb|C|
\item Base packages: base, datasets, grDevices, graphics, methods,
stats, utils
- \item Other packages: MASS~7.2-44, ade4~1.4-9, ape~2.2-1,
+ \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~1.5-3, zoo~1.5-4
- \item Loaded via a namespace (and not attached): grid~2.7.2,
- lattice~0.17-13
+ 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
\end{itemize}
There were two compilation steps:
\begin{itemize}
- \item \Rlogo{} compilation time was: Thu Oct 16 11:18:43 2008
+ \item \Rlogo{} compilation time was: Sun Oct 26 18:25:07 2008
\item \LaTeX{} compilation time was: \today
\end{itemize}
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