[Seqinr-commits] r1789 - www/src/mainmatter
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jun 6 13:32:53 CEST 2014
Author: jeanlobry
Date: 2014-06-06 13:32:53 +0200 (Fri, 06 Jun 2014)
New Revision: 1789
Modified:
www/src/mainmatter/acnucsocket.rnw
www/src/mainmatter/acnucsocket.tex
Log:
book.bib no more distributed with the seqinr package but still on SVN repos
Modified: www/src/mainmatter/acnucsocket.rnw
===================================================================
--- www/src/mainmatter/acnucsocket.rnw 2014-06-06 11:22:53 UTC (rev 1788)
+++ www/src/mainmatter/acnucsocket.rnw 2014-06-06 11:32:53 UTC (rev 1789)
@@ -5,6 +5,7 @@
\author{Penel, S.}
\begin{document}
+\SweaveOpts{concordance=TRUE}
\SweaveInput{../config/commonrnw.rnw}
\maketitle
\tableofcontents
@@ -535,19 +536,7 @@
\vspace{0.2cm}
-For \LaTeX{} users, these references are available in the \texttt{book.bib} file that ships
-with \seqinr{} in the \texttt{seqinr/doc/src/config/} folder. To locate this file on your
-computer try:
-<<showbookbib,fig=F>>=
-(seqinrloc <- normalizePath(.path.package("seqinr")))
-setwd(seqinrloc)
-dir()
-setwd("./doc/src/config")
-dir()
-cat(readLines("book.bib", n = 5), sep = "\n")
-@
-
%
% For Sweave users, go back home:
%
Modified: www/src/mainmatter/acnucsocket.tex
===================================================================
--- www/src/mainmatter/acnucsocket.tex 2014-06-06 11:22:53 UTC (rev 1788)
+++ www/src/mainmatter/acnucsocket.tex 2014-06-06 11:32:53 UTC (rev 1789)
@@ -6,6 +6,7 @@
\usepackage{Sweave}
\begin{document}
+\input{acnucsocket-concordance}
%
% To change the R input/output style:
%
@@ -111,8 +112,8 @@
% Mettre eval=F apres premier download
\begin{Schunk}
\begin{Sinput}
- download.file("ftp://pbil.univ-lyon1.fr/pub/seqinr/demoacnuc/acnucdatabase.tar.Z",
- destfile = "./ACNUC_HOME/ACNUC_DB/demoacnuc/acnucdatabase.tar.Z")
+ download.file("ftp://pbil.univ-lyon1.fr/pub/seqinr/demoacnuc/acnucdatabase.tar.Z",
+ destfile = "./ACNUC_HOME/ACNUC_DB/demoacnuc/acnucdatabase.tar.Z")
\end{Sinput}
\end{Schunk}
@@ -212,8 +213,8 @@
% Mettre eval=F apres premier download
\begin{Schunk}
\begin{Sinput}
- download.file("ftp://pbil.univ-lyon1.fr/pub/acnuc/unix/racnucd.tar",
- destfile = "./ACNUC_HOME/ACNUC_SOFT/racnucd.tar")
+ download.file("ftp://pbil.univ-lyon1.fr/pub/acnuc/unix/racnucd.tar",
+ destfile = "./ACNUC_HOME/ACNUC_SOFT/racnucd.tar")
\end{Sinput}
\end{Schunk}
@@ -237,21 +238,27 @@
dir("./ACNUC_HOME/ACNUC_SOFT/")
\end{Sinput}
\begin{Soutput}
-[1] "racnucd"
+[1] "racnucd" "tools"
\end{Soutput}
\begin{Sinput}
dir("./ACNUC_HOME/ACNUC_SOFT/racnucd/")
\end{Sinput}
\begin{Soutput}
- [1] "bit.c" "dbplaces" "dir_acnuc.h"
- [4] "dir_io.c" "dir_io.h" "execute.c"
- [7] "execute.h" "extract.c" "knowndbs"
-[10] "lngbit.c" "makefile" "md5.c"
-[13] "misc_acnuc.c" "ordre.h" "parser.c"
-[16] "prep_acnuc_requete.c" "pretty_seq.c" "proc_requete.c"
-[19] "racnucd.ini" "requete_acnuc.h" "serveur.c"
-[22] "serveur.h" "simext.h" "use_acnuc.c"
-[25] "utilquery.c" "zsockw.c"
+ [1] "bit.c" "bit.o" "dbplaces"
+ [4] "dir_acnuc.h" "dir_io.c" "dir_io.h"
+ [7] "dir_io.o" "execute.c" "execute.h"
+[10] "execute.o" "extract.c" "extract.o"
+[13] "knowndbs" "lngbit.c" "lngbit.o"
+[16] "makefile" "md5.c" "md5.o"
+[19] "misc_acnuc.c" "misc_acnuc.o" "ordre.h"
+[22] "parser.c" "parser.o" "prep_acnuc_requete.c"
+[25] "prep_acnuc_requete.o" "pretty_seq.c" "pretty_seq.o"
+[28] "proc_requete.c" "proc_requete.o" "racnucd"
+[31] "racnucd.ini" "racnucd.log" "racnucd.new"
+[34] "requete_acnuc.h" "serveur.c" "serveur.h"
+[37] "serveur.o" "simext.h" "use_acnuc.c"
+[40] "use_acnuc.o" "utilquery.c" "utilquery.o"
+[43] "zsockw.c" "zsockw.o"
\end{Soutput}
\end{Schunk}
@@ -265,7 +272,7 @@
dir(pattern = "racnucd")
\end{Sinput}
\begin{Soutput}
-[1] "racnucd" "racnucd.ini"
+[1] "racnucd" "racnucd.ini" "racnucd.log" "racnucd.new"
\end{Soutput}
\begin{Sinput}
setwd(pwd)
@@ -281,8 +288,7 @@
\begin{Schunk}
\begin{Sinput}
- cat(readLines("./ACNUC_HOME/ACNUC_SOFT/racnucd/racnucd.ini"),
- sep = "\n")
+ cat(readLines("./ACNUC_HOME/ACNUC_SOFT/racnucd/racnucd.ini"), sep = "\n")
\end{Sinput}
\begin{Soutput}
port=5558
@@ -307,10 +313,9 @@
\begin{Schunk}
\begin{Sinput}
initline <- readLines("./ACNUC_HOME/ACNUC_SOFT/racnucd/racnucd.ini")
- initline[1] = "port=49152"
+ initline[1]="port=49152"
writeLines(initline, "./ACNUC_HOME/ACNUC_SOFT/racnucd/racnucd.new")
- cat(readLines("./ACNUC_HOME/ACNUC_SOFT/racnucd/racnucd.new"),
- sep = "\n")
+ cat(readLines("./ACNUC_HOME/ACNUC_SOFT/racnucd/racnucd.new"), sep = "\n")
\end{Sinput}
\begin{Soutput}
port=49152
@@ -328,8 +333,7 @@
\begin{Schunk}
\begin{Sinput}
- cat(readLines("./ACNUC_HOME/ACNUC_SOFT/racnucd/knowndbs"),
- sep = "\n")
+ cat(readLines("./ACNUC_HOME/ACNUC_SOFT/racnucd/knowndbs"),sep = "\n")
\end{Sinput}
\begin{Soutput}
embl | on | | EMBL sequence data library |
@@ -390,14 +394,13 @@
\begin{Sinput}
indexpath <- normalizePath("./ACNUC_HOME/ACNUC_DB/demoacnuc/index")
ffpath <- normalizePath("./ACNUC_HOME/ACNUC_DB/demoacnuc/flat_files")
- newdb <- paste("setenv demoacnuc '", indexpath, " ", ffpath,
- "'", sep = "", collapse = "")
+ newdb <- paste("setenv demoacnuc '", indexpath, " ", ffpath, "'", sep = "", collapse = "")
writeLines(newdb, "./ACNUC_HOME/ACNUC_SOFT/racnucd/dbplaces")
dbplaces <- readLines("./ACNUC_HOME/ACNUC_SOFT/racnucd/dbplaces")
cat(dbplaces, sep = "\n")
\end{Sinput}
\begin{Soutput}
-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'
+setenv demoacnuc '/Users/lobry/seqinr/www/src/mainmatter/ACNUC_HOME/ACNUC_DB/demoacnuc/index /Users/lobry/seqinr/www/src/mainmatter/ACNUC_HOME/ACNUC_DB/demoacnuc/flat_files'
\end{Soutput}
\end{Schunk}
@@ -415,16 +418,16 @@
system("ps | grep racnucd", intern = TRUE)
\end{Sinput}
\begin{Soutput}
-[1] "14492 p2 S+ 0:00.01 ./racnucd racnucd.new"
-[2] "14493 p2 S+ 0:00.01 sh -c ps | grep racnucd"
-[3] "14495 p2 S+ 0:00.00 grep racnucd"
+character(0)
+attr(,"status")
+[1] 1
\end{Soutput}
\begin{Sinput}
cat(readLines("racnucd.log"), sep = "\n")
\end{Sinput}
\begin{Soutput}
*******************************************************
-Start of remote acnuc server : Thu Nov 5 14:22:23 2009
+Start of remote acnuc server : Fri Jun 6 13:28:33 2014
\end{Soutput}
\begin{Sinput}
setwd(pwd)
@@ -449,8 +452,9 @@
\begin{Schunk}
\begin{Sinput}
library(seqinr)
+ #system("hostname", intern = TRUE) -> hostname
hostname <- "localhost"
- choosebank(host = hostname, port = 49152, info = TRUE)
+ choosebank(host = hostname,port=49152, info = TRUE)
\end{Sinput}
\begin{Soutput}
bank status
@@ -465,7 +469,7 @@
\begin{Schunk}
\begin{Sinput}
- choosebank(bank = "demoacnuc", host = hostname, port = 49152)
+ choosebank(bank = "demoacnuc",host = hostname,port=49152)
query("mylist", "k=rib@ prot@")
mylist$nelem
\end{Sinput}
@@ -539,8 +543,8 @@
% Mettre eval=F apres premier download
\begin{Schunk}
\begin{Sinput}
- download.file("ftp://pbil.univ-lyon1.fr/pub/acnuc/unix/acnucsoft.tar",
- destfile = "./ACNUC_HOME/ACNUC_SOFT/tools/acnucsoft.tar")
+ download.file("ftp://pbil.univ-lyon1.fr/pub/acnuc/unix/acnucsoft.tar",
+ destfile = "./ACNUC_HOME/ACNUC_SOFT/tools/acnucsoft.tar")
\end{Sinput}
\end{Schunk}
@@ -577,21 +581,23 @@
[7] "bit.c" "bit.o" "compressnewdiv.c"
[10] "connectindex.c" "conv_to_bigannots.c" "coperations.c"
[13] "dir_acnuc.h" "dir_io.c" "dir_io.h"
-[16] "dir_io.o" "dynlist.c" "dynlist.o"
-[19] "extract.c" "fortran_ex.f" "gestion_acnuc.c"
-[22] "gestion_acnuc.o" "hashacc.c" "hashacc.o"
-[25] "initf.c" "libcacnuc.a" "lngbit.c"
-[28] "lngbit.o" "makefile" "mdshrt_lng.c"
-[31] "mdshrt_lng.o" "misc_acnuc.c" "misc_acnuc.o"
-[34] "ncbitaxo.h" "newordalphab.c" "pretty_seq.c"
-[37] "proc_requete.c" "query.c" "readncbitaxo.c"
-[40] "renamediv.c" "simext.h" "smjytload.c"
-[43] "sortsubseq.c" "supold.c" "testmatchindex.c"
-[46] "two_banks.c" "two_banks.o" "updatehelp.c"
-[49] "use_acnuc.c" "use_acnuc.o" "utilgener.c"
-[52] "utilgener.h" "utilgener.o" "utilgener2.c"
-[55] "utilgener2.o" "utilquery.c" "utilquery.o"
-[58] "voyage.c"
+[16] "dir_io.o" "extract.c" "extract.o"
+[19] "fortran_ex.f" "gestion_acnuc.c" "gestion_acnuc.o"
+[22] "hashacc.c" "hashacc.o" "initf.c"
+[25] "libcacnuc.a" "lngbit.c" "lngbit.o"
+[28] "makefile" "mdshrt_lng.c" "mdshrt_lng.o"
+[31] "misc_acnuc.c" "misc_acnuc.o" "ncbitaxo.h"
+[34] "newordalphab.c" "pretty_seq.c" "pretty_seq.o"
+[37] "proc_requete.c" "proc_requete.o" "query"
+[40] "query.c" "query.o" "readncbitaxo.c"
+[43] "readncbitaxo.o" "readtaxdump.c" "readtaxdump.o"
+[46] "renamediv.c" "simext.h" "smjytload.c"
+[49] "sortsubseq.c" "supold.c" "testmatchindex.c"
+[52] "two_banks.c" "two_banks.o" "updatehelp.c"
+[55] "use_acnuc.c" "use_acnuc.o" "utilgener.c"
+[58] "utilgener.h" "utilgener.o" "utilgener2.c"
+[61] "utilgener2.o" "utilquery.c" "utilquery.o"
+[64] "voyage.c"
\end{Soutput}
\begin{Sinput}
setwd(pwd)
@@ -636,8 +642,8 @@
% Mettre eval=F apres premier download
\begin{Schunk}
\begin{Sinput}
- download.file("ftp://pbil.univ-lyon1.fr/pub/seqinr/demoacnuc/escherichia_uniprot.dat.Z",
- destfile = "./ACNUC_HOME/ACNUC_DB/mydb/flat_files/escherichia_uniprot.dat.Z")
+ download.file("ftp://pbil.univ-lyon1.fr/pub/seqinr/demoacnuc/escherichia_uniprot.dat.Z",
+ destfile = "./ACNUC_HOME/ACNUC_DB/mydb/flat_files/escherichia_uniprot.dat.Z")
\end{Sinput}
\end{Schunk}
@@ -669,30 +675,30 @@
% Mettre eval=F apres premier download
\begin{Schunk}
\begin{Sinput}
- download.file("ftp://pbil.univ-lyon1.fr/pub/seqinr/demoacnuc/buildindex.csh",
- destfile = "./ACNUC_HOME/ACNUC_DB/mydb/buildindex.csh")
+ download.file("ftp://pbil.univ-lyon1.fr/pub/seqinr/demoacnuc/buildindex.csh",
+ destfile = "./ACNUC_HOME/ACNUC_DB/mydb/buildindex.csh")
setwd("./ACNUC_HOME/ACNUC_DB/mydb/")
system("chmod +x ./buildindex.csh")
system("./buildindex.csh escherichia_uniprot > ./build.log")
- cat(readLines("build.log", 50), sep = "\n")
+ cat(readLines("build.log",50), sep = "\n")
\end{Sinput}
\begin{Soutput}
Build a protein database in:
============================
- ->/Users/lobry/seqinr/pkg/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb
+ ->/Users/lobry/seqinr/www/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb
ACNUC environment:
- ->/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
+ ->/Users/lobry/seqinr/www/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/index
+ ->/Users/lobry/seqinr/www/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/flat_files
ACNUC tools in:
- ->/Users/lobry/seqinr/pkg/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/../../ACNUC_SOFT/tools
+ ->/Users/lobry/seqinr/www/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/../../ACNUC_SOFT/tools
flat file: escherichia_uniprot.dat
- ->/Users/lobry/seqinr/pkg/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/flat_files/escherichia_uniprot.dat
+ ->/Users/lobry/seqinr/www/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/flat_files/escherichia_uniprot.dat
Begin to build index...
-Thu Nov 5 14:22:43 CET 2009
+Ven 6 jui 2014 13:28:43 CEST
=====================================
Initialise
@@ -705,7 +711,7 @@
=====================================
run updatehelp
-Thu Nov 5 14:22:43 CET 2009
+Ven 6 jui 2014 13:28:43 CEST
Index have been sucessfully build.
=====================================
@@ -713,25 +719,25 @@
==================
\end{Soutput}
\begin{Sinput}
- cat(tail(readLines("build.log"), 50), sep = "\n")
+ cat(tail(readLines("build.log"),50), sep = "\n")
\end{Sinput}
\begin{Soutput}
Build a protein database in:
============================
- ->/Users/lobry/seqinr/pkg/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb
+ ->/Users/lobry/seqinr/www/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb
ACNUC environment:
- ->/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
+ ->/Users/lobry/seqinr/www/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/index
+ ->/Users/lobry/seqinr/www/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/flat_files
ACNUC tools in:
- ->/Users/lobry/seqinr/pkg/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/../../ACNUC_SOFT/tools
+ ->/Users/lobry/seqinr/www/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/../../ACNUC_SOFT/tools
flat file: escherichia_uniprot.dat
- ->/Users/lobry/seqinr/pkg/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/flat_files/escherichia_uniprot.dat
+ ->/Users/lobry/seqinr/www/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/flat_files/escherichia_uniprot.dat
Begin to build index...
-Thu Nov 5 14:22:43 CET 2009
+Ven 6 jui 2014 13:28:43 CEST
=====================================
Initialise
@@ -744,7 +750,7 @@
=====================================
run updatehelp
-Thu Nov 5 14:22:43 CET 2009
+Ven 6 jui 2014 13:28:43 CEST
Index have been sucessfully build.
=====================================
@@ -836,46 +842,7 @@
\vspace{0.2cm}
-For \LaTeX{} users, these references are available in the \texttt{book.bib} file that ships
-with \seqinr{} in the \texttt{seqinr/doc/src/config/} folder. To locate this file on your
-computer try:
-\begin{Schunk}
-\begin{Sinput}
- (seqinrloc <- normalizePath(.path.package("seqinr")))
-\end{Sinput}
-\begin{Soutput}
-[1] "/Users/lobry/seqinr/pkg.Rcheck/seqinr"
-\end{Soutput}
-\begin{Sinput}
- setwd(seqinrloc)
- dir()
-\end{Sinput}
-\begin{Soutput}
- [1] "abif" "CITATION" "data" "DESCRIPTION" "doc"
- [6] "help" "html" "INDEX" "libs" "Meta"
-[11] "R" "sequences"
-\end{Soutput}
-\begin{Sinput}
- setwd("./doc/src/config")
- dir()
-\end{Sinput}
-\begin{Soutput}
-[1] "atxy.sty" "authors.tex" "book.bib" "commonrnw.rnw"
-[5] "commontex.tex" "sessionInfo.rnw"
-\end{Soutput}
-\begin{Sinput}
- cat(readLines("book.bib", n = 5), sep = "\n")
-\end{Sinput}
-\begin{Soutput}
- at incollection{seqinr,
- author = {Charif, D. and Lobry, J.R.},
- 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},
-\end{Soutput}
-\end{Schunk}
-
%
% For Sweave users, go back home:
%
@@ -888,20 +855,20 @@
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, tools~2.10.0
+ \item Other packages: ade4~1.6-2, ape~3.1-2, grImport~0.9-0,
+ MASS~7.3-31, seqinr~3.0-11, 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: Thu Nov 5 14:22:43 2009
+ \item \Rlogo{} compilation time was: Fri Jun 6 13:28:43 2014
\item \LaTeX{} compilation time was: \today
\end{itemize}
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