[Seqinr-commits] r1585 - pkg/inst/doc/src/mainmatter
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Apr 23 11:55:42 CEST 2009
Author: lobry
Date: 2009-04-23 11:55:42 +0200 (Thu, 23 Apr 2009)
New Revision: 1585
Modified:
pkg/inst/doc/src/mainmatter/acnucsocket.tex
Log:
R 2.9.0 compilation
Modified: pkg/inst/doc/src/mainmatter/acnucsocket.tex
===================================================================
--- pkg/inst/doc/src/mainmatter/acnucsocket.tex 2009-04-23 09:52:30 UTC (rev 1584)
+++ pkg/inst/doc/src/mainmatter/acnucsocket.tex 2009-04-23 09:55:42 UTC (rev 1585)
@@ -4,7 +4,7 @@
\title{Installation of a local ACNUC socket server and of a local ACNUC database on your machine.}
\author{Penel, S.}
-\usepackage{/Library/Frameworks/R.framework/Resources/share/texmf/Sweave}
+\usepackage{Sweave}
\begin{document}
%
% To change the R input/output style:
@@ -415,16 +415,16 @@
system("ps | grep racnucd", intern = TRUE)
\end{Sinput}
\begin{Soutput}
-[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"
+[1] "27474 p2 S+ 0:00.01 ./racnucd racnucd.new"
+[2] "27475 p2 S+ 0:00.01 sh -c ps | grep racnucd"
+[3] "27477 p2 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 : Sun Oct 26 18:13:16 2008
+Start of remote acnuc server : Thu Apr 23 11:53:08 2009
\end{Soutput}
\begin{Sinput}
setwd(pwd)
@@ -572,33 +572,26 @@
dir()
\end{Sinput}
\begin{Soutput}
- [1] "acnuc2fasta" "acnuc2fasta.c" "acnucf2c.c"
- [4] "acnucf2c.o" "acnucgener" "acnucgener.c"
- [7] "arbrebin.c" "arbrebin.o" "bit.c"
-[10] "bit.o" "compressnewdiv" "compressnewdiv.c"
-[13] "connectindex" "connectindex.c" "conv_to_bigannots"
-[16] "conv_to_bigannots.c" "coperations.c" "dir_acnuc.h"
-[19] "dir_io.c" "dir_io.h" "dir_io.o"
-[22] "dynlist.c" "dynlist.o" "extract.c"
-[25] "extract.o" "fortran_ex.f" "gestion_acnuc.c"
-[28] "gestion_acnuc.o" "hashacc.c" "hashacc.o"
-[31] "initf" "initf.c" "libcacnuc.a"
-[34] "lngbit.c" "lngbit.o" "makefile"
-[37] "mdshrt_lng.c" "mdshrt_lng.o" "misc_acnuc.c"
-[40] "misc_acnuc.o" "ncbitaxo.h" "newordalphab"
-[43] "newordalphab.c" "pretty_seq.c" "pretty_seq.o"
-[46] "proc_requete.c" "proc_requete.o" "query"
-[49] "query.c" "query.o" "readidreport.c"
-[52] "readidreport.o" "readncbitaxo" "readncbitaxo.c"
-[55] "renamediv" "renamediv.c" "simext.h"
-[58] "smjytload" "smjytload.c" "sortsubseq"
-[61] "sortsubseq.c" "supold" "supold.c"
-[64] "testmatchindex" "testmatchindex.c" "two_banks.c"
-[67] "two_banks.o" "updatehelp" "updatehelp.c"
-[70] "use_acnuc.c" "use_acnuc.o" "utilgener.c"
-[73] "utilgener.h" "utilgener.o" "utilgener2.c"
-[76] "utilgener2.o" "utilquery.c" "utilquery.o"
-[79] "voyage" "voyage.c"
+ [1] "acnuc2fasta.c" "acnucf2c.c" "acnucf2c.o"
+ [4] "acnucgener.c" "arbrebin.c" "arbrebin.o"
+ [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"
\end{Soutput}
\begin{Sinput}
setwd(pwd)
@@ -699,96 +692,64 @@
->/Users/lobry/seqinr/pkg/inst/doc/src/mainmatter/ACNUC_HOME/ACNUC_DB/mydb/flat_files/escherichia_uniprot.dat
Begin to build index...
-Sun Oct 26 18:13:52 CET 2008
+Thu Apr 23 11:53:24 CEST 2009
=====================================
Initialise
-Normal end.
=====================================
Generation des index
-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 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 Sun Oct 26 18:13:53 2008
+=====================================
+run newordalphab
----->3MG1_ECOLI
----->3MG2_ECOLI
----->6PGD_ECOLI
----->6PGL_ECOLI
----->A4UR75_ECOLI
----->A4UR76_ECOLI
----->A4UR77_ECOLI
----->A4UR78_ECOLI
----->A4UR79_ECOLI
----->A4UR80_ECOLI
----->A4UR81_ECOLI
----->A4UR83_ECOLI
----->A4UR84_ECOLI
----->A4UR86_ECOLI
----->A5A605_ECOLI
----->A5A607_ECOLI
----->A5A609_ECOLI
+
+=====================================
+run updatehelp
+Thu Apr 23 11:53:24 CEST 2009
+Index have been sucessfully build.
+=====================================
+
+Testing the index:
+==================
\end{Soutput}
\begin{Sinput}
cat(tail(readLines("build.log"), 50), sep = "\n")
\end{Sinput}
\begin{Soutput}
-Program finished at Sun Oct 26 18:13:56 2008
+ Build a protein database in:
+ ============================
+ ->/Users/lobry/seqinr/pkg/inst/doc/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
+
+ACNUC tools in:
+ ->/Users/lobry/seqinr/pkg/inst/doc/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
+
+Begin to build index...
+Thu Apr 23 11:53:24 CEST 2009
+=====================================
+Initialise
-write_quick_meres...done
+=====================================
+Generation des index
-lues=4461 chargees=4461 difference=0
-seqs/second=1487.00
-
=====================================
run newordalphab
-Sorting file SUBSEQ.NEW
-Writing list of loci and unvalid seqs
-Sorting file SMJYT.NEW
-Computing sequence hashing
-Writing SPECIES.NEW
-Writing KEYWORDS.NEW
-Writing hashing data
-Short lists of keywords and info records
-Sorting file ACCESS.NEW
-Sorting file BIBLIO.NEW
-Writing LOCUS.NEW and lists of access#s and refers
-Sorting file AUTHOR.NEW
-Writing lists of seqs and authors for refers
-Writing lists of refers for authors
-Writing tree structure of keywords
-Writing tree structure of species
-Replacing old index files by new ones
-Normal end
=====================================
run updatehelp
-Sun Oct 26 18:13:58 CET 2008
+Thu Apr 23 11:53:24 CEST 2009
Index have been sucessfully build.
=====================================
Testing the index:
==================
-Opening a flat database in 2 divisions
-Sorry, no help available for this command: CONT
-[27 free lists available]
-
-Command? (or H for help)
-Enter your selection criteria, or H(elp) (EX: sp=equus and k=globin@)
-List LIST1 contains 4461 sequences
-
-Command? (or H for help)
-List name, or H(elp) ? [LIST1] Name of file to write list content? [default= list1.mne]
-Command? (or H for help)
-End of ACNUC retrieval program
- 4461 4461 93681 test.mn
\end{Soutput}
\begin{Sinput}
setwd(pwd)
@@ -892,16 +853,17 @@
\end{Sinput}
\begin{Soutput}
[1] "CITATION" "CONTENTS" "DESCRIPTION" "INDEX" "Meta"
- [6] "R" "R-ex" "data" "doc" "help"
-[11] "html" "latex" "libs" "man" "sequences"
+ [6] "R" "R-ex" "abif" "data" "doc"
+[11] "help" "html" "latex" "libs" "man"
+[16] "sequences"
\end{Soutput}
\begin{Sinput}
setwd("./doc/src/config")
dir()
\end{Sinput}
\begin{Soutput}
-[1] "atxy.sty" "book.bib" "commonrnw.rnw" "commontex.tex"
-[5] "sessionInfo.rnw"
+[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")
@@ -922,26 +884,30 @@
\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|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, grDevices, graphics, 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, tools~2.9.0
\end{itemize}
There were two compilation steps:
\begin{itemize}
- \item \Rlogo{} compilation time was: Sun Oct 26 18:13:58 2008
+ \item \Rlogo{} compilation time was: Thu Apr 23 11:53:24 2009
\item \LaTeX{} compilation time was: \today
\end{itemize}
+\end{scriptsize}
+
% END - DO NOT REMOVE THIS LINE
%%%%%%%%%%%% BIBLIOGRAPHY %%%%%%%%%%%%%%%%%
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