[Seqinr-commits] r1529 - pkg/man

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

Author: lobry
Date: 2009-01-21 10:24:23 +0100 (Wed, 21 Jan 2009)
New Revision: 1529

Modified:
   pkg/man/SEQINR.UTIL.Rd
   pkg/man/consensus.Rd
   pkg/man/dia.bactgensize.Rd
   pkg/man/getTrans.Rd
   pkg/man/modifylist.Rd
   pkg/man/read.alignment.Rd
   pkg/man/readfirstrec.Rd
Log:
OK compil 2.8.1

Modified: pkg/man/SEQINR.UTIL.Rd
===================================================================
--- pkg/man/SEQINR.UTIL.Rd	2009-01-21 09:22:27 UTC (rev 1528)
+++ pkg/man/SEQINR.UTIL.Rd	2009-01-21 09:24:23 UTC (rev 1529)
@@ -8,7 +8,7 @@
 \usage{data(SEQINR.UTIL)}
 \format{
  	\code{SEQINR.UTIL} is a list containing the 4 following objects:  
-	\enumerate{	
+	\describe{	
  	\item{CODES.NCBI}{is a data frame containing the genetics code : The standard ('Universal') genetic code with a selection of non-standard codes. } 
  	\item{CODON.AA}{is a three columns data frame. The first column is a factor containing the codon. The second column is a factor giving the aminoacids names for each codon. The last column is a factor giving the IUPAC one-letter code for aminoacids}
  	\item{AA.PROPERTY}{is a list giving the physico-chemical class of amino acid. The differents classes are the following one : Tiny, Small, Aliphatic, Aromatic, Non.polar, Polar, Charged, Basic, Acidic }

Modified: pkg/man/consensus.Rd
===================================================================
--- pkg/man/consensus.Rd	2009-01-21 09:22:27 UTC (rev 1528)
+++ pkg/man/consensus.Rd	2009-01-21 09:24:23 UTC (rev 1529)
@@ -26,7 +26,7 @@
    to \code{\link{bma}}.}
 }
 \details{
-  \enumerate{
+  \describe{
   \item{"majority"}{The character with the higher frequency is returned as the
   consensus character.}
 

Modified: pkg/man/dia.bactgensize.Rd
===================================================================
--- pkg/man/dia.bactgensize.Rd	2009-01-21 09:22:27 UTC (rev 1528)
+++ pkg/man/dia.bactgensize.Rd	2009-01-21 09:24:23 UTC (rev 1529)
@@ -35,11 +35,11 @@
 }
 \value{
   An invisible dataframe with three components:
-  \enumerate{
+
   \item{genus }{genus name}
   \item{species }{species names}
   \item{gs }{genome size in Kb}
-  }
+  
 }
 \references{
 Please cite the following references when using data from GOLD:

Modified: pkg/man/getTrans.Rd
===================================================================
--- pkg/man/getTrans.Rd	2009-01-21 09:22:27 UTC (rev 1528)
+++ pkg/man/getTrans.Rd	2009-01-21 09:24:23 UTC (rev 1529)
@@ -35,7 +35,7 @@
 \details{
  The following genetic codes are described here. The number preceding each code 
  corresponds to \code{numcode}. 
-  \enumerate{
+  \describe{
   \item{1}{ standard }
   \item{2}{ vertebrate.mitochondrial }
   \item{3}{ yeast.mitochondrial }

Modified: pkg/man/modifylist.Rd
===================================================================
--- pkg/man/modifylist.Rd	2009-01-21 09:22:27 UTC (rev 1528)
+++ pkg/man/modifylist.Rd	2009-01-21 09:24:23 UTC (rev 1529)
@@ -24,7 +24,7 @@
 \details{
 Example of possible values for the argument \code{operation}: 
 
-  \enumerate{
+  \describe{
   \item{length}{as in  "> 10000"    or    "< 500"}
   \item{date}{as in   "> 1/jul/2001"   or   "< 30/AUG/98"}
   \item{scan}{specify the string to be searched for}
@@ -36,10 +36,6 @@
 The result is directly assigned to the object \code{modlistname} in the user workspace.
 This is an objet of class \code{qaw}, a list with the following 6 components:
 
-The result is directly assigned to the object \code{listname} in the user workspace.
-This is an objet of class \code{qaw}, a list with the following 6 components:
-
-  \enumerate{
   \item{call}{the original call}
   \item{name}{the ACNUC list name}
   \item{nelem}{the number of elements (for instance sequences) in the ACNUC list}
@@ -48,7 +44,7 @@
   \item{req}{a list of sequence names that fit the required criteria or \code{NA} when
     called with parameter \code{virtual} is \code{TRUE}}
   \item{socket}{the socket connection that was used}
-  }
+  
 }
 \references{ \url{http://pbil.univ-lyon1.fr/databases/acnuc.html}
 

Modified: pkg/man/read.alignment.Rd
===================================================================
--- pkg/man/read.alignment.Rd	2009-01-21 09:22:27 UTC (rev 1528)
+++ pkg/man/read.alignment.Rd	2009-01-21 09:24:23 UTC (rev 1529)
@@ -21,7 +21,7 @@
     As from seqinR 1.1-3 this argument is deprecated and a warning is issued.}
 }
 \details{
-  \enumerate{
+  \describe{
    \item{"mase"}{The mase format is used to store nucleotide or protein 
    multiple alignments. The beginning of the file must contain a header 
    containing at least one line (but the content of this header may be 

Modified: pkg/man/readfirstrec.Rd
===================================================================
--- pkg/man/readfirstrec.Rd	2009-01-21 09:22:27 UTC (rev 1528)
+++ pkg/man/readfirstrec.Rd	2009-01-21 09:24:23 UTC (rev 1529)
@@ -17,7 +17,7 @@
 \details{
 Available index files are:
 
-  \enumerate{
+  \describe{
 	\item{AUT}{AUTHOR one record for each author name (last name only, no initials)}
 	\item{BIB}{BIBLIO one record for each reference}
 	\item{ACC}{ACCESS one record for each accession number}